</head> <body>Authors: <br/> Arnau Montagud, Barcelona Supercomputing Center, Spain <br/> <br/> Miguel Ponce de Leon, Barcelona Supercomputing Center, Spain <br/> <br/> Description: Molecular mechanisms affected by Nsp4 and Nsp6 proteins of SARS-CoV-2 </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:modelVersion>4.0</celldesigner:modelVersion> <celldesigner:modelDisplay sizeX="3200" sizeY="2000"/> <celldesigner:listOfIncludedSpecies> <celldesigner:species id="s145" name="TOMM70"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> UNIPROT:O94826 </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s70</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr24</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> 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name="TOMM5"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> UNIPROT:Q8N4H5 </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s70</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr19</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s141" name="TOMM7"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> UNIPROT:Q9P0U1 </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s70</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr20</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s142" name="TOMM20"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> UNIPROT:Q15388 </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s70</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr21</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s143" name="TOMM22"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> UNIPROT:Q9NS69 </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s70</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr22</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s144" name="TOMM40"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> UNIPROT:O96008 </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s70</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr23</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s176" name="TIMM29"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> UNIPORT:Q9BSF4 FUNCTION:Component of the TIM22 complex, a complex that mediates the import and insertion of multi-pass transmembrane proteins into the mitochondrial inner membrane. </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s112</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr8</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s177" name="TIMM22"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> UNIPROT:Q9Y584 FUNCTION:Essential core component of the TIM22 complex, a complex that mediates the import and insertion of multi-pass transmembrane proteins into the mitochondrial inner membrane. In the TIM22 complex, it constitutes the voltage-activated and signal-gated channel. Forms a twin-pore translocase that uses the membrane potential as external driving force in 2 voltage-dependent steps (By similarity). </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s112</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr15</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s178" name="TIMM10B"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> UNIPROT:Q9Y5J6 FUNCTION:Component of the TIM22 complex, a complex that mediates the import and insertion of multi-pass transmembrane proteins into the mitochondrial inner membrane. The TIM22 complex forms a twin-pore translocase that uses the membrane potential as the external driving force. In the TIM22 complex, it may act as a docking point for the soluble 70 kDa complex that guides the target proteins in transit through the aqueous mitochondrial intermembrane space. </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s112</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr10</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s179" name="TIMM9"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> UNIPROT:Q9Y5J7 FUNCTION:Mitochondrial intermembrane chaperone that participates in the import and insertion of multi-pass transmembrane proteins into the mitochondrial inner membrane. </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s112</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr2</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s180" name="TIMM10"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> UNIPROT:P62072 FUNCTION:Mitochondrial intermembrane chaperone that participates in the import and insertion of multi-pass transmembrane proteins into the mitochondrial inner membrane. May also be required for the transfer of beta-barrel precursors from the TOM complex to the sorting and assembly machinery (SAM complex) of the outer membrane. 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Guides the V-type ATPase into specialized subcellular compartments </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s213</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr14</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s232" name="ATP6AP1"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> V-Type Proton ATPase Subunit S1 </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s249</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr14</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s233" name="Nsp6"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body/> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s249</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr3</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s238" name="ATP6AP1"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> V-Type Proton ATPase Subunit S1 </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s247</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr14</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> 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<celldesigner:species id="s298" name="Nsp6"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body/> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s257</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr3</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s299" name="ATP13A3"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body/> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s257</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr5</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s295" name="ATP13A3"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> UNIPROT:Q9H7F0 FUNCTION:Probable cation-transporting ATPase 13A3 </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s264</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr5</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s307" name="NUP210"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> UNIPROT:Q8TEM1 FUNCTION: Nucleoporin essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as structural integrity. (DOI: 10.1091/mbc.e03-04-0260) </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s306</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr7</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s308" name="Selinexor"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> [PMID:32353859] </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s306</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>DRUG</celldesigner:class> <celldesigner:name>Selinexor</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s316" name="SLC6A15"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body/> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s315</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr32</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s317" name="SLC6A15"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body/> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s313</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr32</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s318" name="SLC6A15"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body/> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s311</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr32</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s319" name="Nsp6"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> UniProt: P0DTC6 NS6_SARS2 Non-structural protein Nsp6 limits autophagasome expansion. Nsp6 may favor SARS-CoV infection by compromising the ability of autophagosomes to deliver lysosomes for degradation -Complexes with Nsp3 and Nsp4 to form double-membrane vesicles that anchor viral replication complexes. [PMID: 32353859] From SARS-COV-1: Coronavirus nsp6 is a multipass transmembrane protein implicated in the formation of DMVs during SARS-CoV infection (1). Overexpression of nsp6 of IBV, MHV, or SARS-CoV activated the formation of autophagosomes from the ER via an omegasome intermediate (18). However, autophagosomes induced by IBV infection or overexpression of coronavirus nsp6 had smaller diameters compared with those induced by starvation, indicating that nsp6 might also restrict the expansion of autophagosomes (19). [PMID: 31226023] </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s311</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr3</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s320" name="Orf9c"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body/> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s313</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr33</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s321" name="M"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body/> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s315</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr34</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s324" name="SLC6A15"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> While SLC15A3 was not identified as an interactor of Orf3a, we identified interactions between SARS-CoV-2 proteins and other members of the solute carrier superfamily including SLC25A17 (SARS-CoV-2 Orf9b and Orf9c) and SLC6A15 (SARS-CoV-2 Orf9c, M and Nsp6), although these interactions fall below our scoring thresholds [PMID: 32353859] </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s323</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr32</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s335" name="Bafilomycin A1"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> Gordon [PMID:9572882] </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s326</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>DRUG</celldesigner:class> <celldesigner:name>Bafilomycin A1</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s336" name="ATP6AP1"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> UNIPROT:Q15904 V-Type Proton ATPase Subunit S1 Subunit of the vacuolar ATP synthase protein pump. Dysregulation results in impaired vesicle acidification and intracytoplasmic granules, resulting in a range of pathologies including an immunodeficiency syndrome and granular cell tumors. Identified as a potential host factor for IAV, WNV, and DENV. [PMID: 32353859] </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s326</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr14</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s340" name="ATP6AP1"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> UNIPROT:Q15904 V-Type Proton ATPase Subunit S1 </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s226</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr14</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s346" name="SIGMAR1"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> UNIPROT:Q99720 FUNCTION:Functions in lipid transport from the endoplasmic reticulum and is involved in a wide array of cellular functions probably through regulation of the biogenesis of lipid microdomains at the plasma membrane. (DOI:10.1074/jbc.272.43.27107) Sigma Receptor 1 is an ER chaperone protein that modulates calcium signaling through its interaction with the IP3 receptor. It is targeted by a number of existing drugs including Chloroquine and haloperidol. [PMID: 32353859] </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s345</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr13</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s348" name="Several drugs"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> SIGMAR interacts with many drugs: BD1008, Carbapentane, Chloroquine, Clemastine, Cloperastine, Dextromethorphan, E-52862, Haloperidol, Hydroxychloroquine, Ifenprodil, Olanzapine, PB28, PD-144418, Pimozide, Progesterone, Rimcazole, RS-PPCC, Siramesine [PMID: 32353859] </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s345</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>DRUG</celldesigner:class> 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<celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr6</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s356" name="Nsp4"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> Non-structural protein 4 Nsp4 forms a complex with Nsp3 and Nsp6. [PMID: 32353859] </body> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s294</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr1</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s30" name="IDE"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body/> </html> </celldesigner:notes> <celldesigner:annotation> <celldesigner:complexSpecies>s294</celldesigner:complexSpecies> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr6</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:annotation> </celldesigner:species> <celldesigner:species id="s403" name="Nsp6"> <celldesigner:notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> 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<celldesigner:protein id="pr13" name="SIGMAR1" type="GENERIC"/> <celldesigner:protein id="pr14" name="ATP6AP1" type="GENERIC"/> <celldesigner:protein id="pr15" name="TIMM22" type="GENERIC"/> <celldesigner:protein id="pr19" name="TOMM5" type="GENERIC"/> <celldesigner:protein id="pr20" name="TOMM7" type="GENERIC"/> <celldesigner:protein id="pr21" name="TOMM20" type="GENERIC"/> <celldesigner:protein id="pr22" name="TOMM22" type="GENERIC"/> <celldesigner:protein id="pr23" name="TOMM40" type="GENERIC"/> <celldesigner:protein id="pr24" name="TOMM70" type="GENERIC"/> <celldesigner:protein id="pr27" name="Nsp3" type="GENERIC"/> <celldesigner:protein id="pr32" name="SLC6A15" type="GENERIC"/> <celldesigner:protein id="pr33" name="Orf9c" type="GENERIC"/> <celldesigner:protein id="pr34" name="M" type="GENERIC"/> <celldesigner:protein id="p_s_id_sa8398" name="ATP6V1B1" type="GENERIC"/> <celldesigner:protein id="p_s_id_sa8402" name="ATP6V1E2" type="GENERIC"/> <celldesigner:protein id="p_s_id_sa8396" name="ATP6V1B2" type="GENERIC"/> <celldesigner:protein id="p_s_id_sa8397" name="ATP6V1A" type="GENERIC"/> <celldesigner:protein id="p_s_id_sa8399" name="ATP6V1C1" type="GENERIC"/> <celldesigner:protein id="p_s_id_sa8405" name="ATP6V1H" type="GENERIC"/> <celldesigner:protein id="p_s_id_sa8401" name="ATP6V1E1" type="GENERIC"/> <celldesigner:protein id="p_s_id_sa8403" name="ATP6V1G1" type="GENERIC"/> <celldesigner:protein id="p_s_id_sa8400" name="ATP6V1D" type="GENERIC"/> <celldesigner:protein id="p_s_id_sa8406" name="ATP6V1C2" type="GENERIC"/> <celldesigner:protein id="p_s_id_sa8404" name="ATP6V1G2" type="GENERIC"/> <celldesigner:protein id="p_s_id_sa8413" name="ATP6V0E1" type="GENERIC"/> <celldesigner:protein id="p_s_id_sa8408" name="ATP6V0A2" type="GENERIC"/> <celldesigner:protein id="p_s_id_sa8411" name="ATP6V0D1" type="GENERIC"/> <celldesigner:protein id="p_s_id_sa8407" name="ATP6V0A1" type="GENERIC"/> <celldesigner:protein id="p_s_id_sa8410" name="ATP6V0B" type="GENERIC"/> <celldesigner:protein id="p_s_id_sa8412" name="ATP6V0D2" type="GENERIC"/> <celldesigner:protein id="p_s_id_sa8409" name="ATP6V0C" type="GENERIC"/> <celldesigner:protein id="p_s_id_sa8415" name="ATP6V0E2" type="GENERIC"/> <celldesigner:protein id="p_s_id_sa8414" name="TCIRG1" type="GENERIC"/> </celldesigner:listOfProteins> <celldesigner:listOfGenes/> <celldesigner:listOfRNAs> <celldesigner:RNA id="rn1" name="Nsp4 (+)" type="RNA"/> <celldesigner:RNA id="rn2" name="Nsp6 (+)" type="RNA"/> <celldesigner:RNA id="rn3" name="Nsp3 (+)" type="RNA"/> <celldesigner:RNA id="rn4" name="Nsp6 (-)" type="RNA"/> <celldesigner:RNA id="rn5" name="Nsp3 (-)" type="RNA"/> <celldesigner:RNA id="rn6" name="Nsp4 (-)" type="RNA"/> </celldesigner:listOfRNAs> <celldesigner:listOfAntisenseRNAs/> <celldesigner:listOfLayers/> <celldesigner:listOfBlockDiagrams/> </celldesigner:extension> </annotation> <listOfUnitDefinitions> <unitDefinition metaid="substance" id="substance" name="substance"> <listOfUnits> <unit metaid="CDMT00141" kind="mole"/> </listOfUnits> </unitDefinition> <unitDefinition metaid="volume" id="volume" name="volume"> <listOfUnits> <unit metaid="CDMT00150" kind="litre"/> </listOfUnits> </unitDefinition> <unitDefinition metaid="area" id="area" name="area"> <listOfUnits> <unit metaid="CDMT00151" kind="metre" exponent="2"/> </listOfUnits> </unitDefinition> <unitDefinition metaid="length" id="length" name="length"> <listOfUnits> <unit metaid="CDMT00152" kind="metre"/> </listOfUnits> </unitDefinition> <unitDefinition metaid="time" id="time" name="time"> <listOfUnits> <unit metaid="CDMT00153" kind="second"/> </listOfUnits> </unitDefinition> </listOfUnitDefinitions> <listOfCompartments> <compartment metaid="default" id="default" size="1" units="volume"/> <compartment metaid="c5" id="c5" name="nucleus" size="1" units="volume" outside="c9"> <annotation> <celldesigner:extension> <celldesigner:name>nucleus</celldesigner:name> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#c5"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0005634"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> <compartment metaid="c7" id="c7" name="endosome" size="1" units="volume" outside="c9"> <annotation> <celldesigner:extension> <celldesigner:name>endosome</celldesigner:name> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#c7"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0005768"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> <compartment metaid="c10" id="c10" name="human host" size="1" units="volume" outside="default"> <annotation> <celldesigner:extension> <celldesigner:name>human host</celldesigner:name> </celldesigner:extension> </annotation> </compartment> <compartment metaid="c9" id="c9" name="cell" size="1" units="volume" outside="c10"> <annotation> <celldesigner:extension> <celldesigner:name>cell</celldesigner:name> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#c9"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0005737"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> <compartment metaid="c2" id="c2" name="endoplasmic reticulum" size="1" units="volume" outside="c9"> <annotation> <celldesigner:extension> <celldesigner:name>endoplasmic reticulum</celldesigner:name> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#c2"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0005783"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> <compartment metaid="c3" id="c3" name="mitochondrial matrix" size="1" units="volume" outside="c4"> <annotation> <celldesigner:extension> <celldesigner:name>mitochondrial matrix</celldesigner:name> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#c3"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0005759"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> <compartment metaid="c4" id="c4" name="mitochondrion" size="1" units="volume" outside="c9"> <annotation> <celldesigner:extension> <celldesigner:name>mitochondrion</celldesigner:name> </celldesigner:extension> </annotation> </compartment> <compartment metaid="c8" id="c8" name="double membrane vesicle viral factory" size="1" units="volume" outside="c9"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>double-membrane vesicles (DMV) from ER. From SARS-COV-1: The RTC is associated with modified host ER membranes that produce convoluted membranes (CMs) and double-membrane vesicles (DMVs) in SARS-CoV-, MHV (mouse hepatitis virus)- as well as MERS-CoV-infected cells (Snijder et al., 2006, Knoops et al., 2008, Hagemeijer et al., 2011, de Wilde et al., 2013). [PMID:29128390] From SARS-COV-1: Together, nsp3, nsp4, and nsp6 have the ability to induce double-membrane vesicles that are similar to those observed in SARS coronavirus-infected cells. [PMID:23943763] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:name>double membrane vesicle viral factory</celldesigner:name> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#c8"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0039718"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> </listOfCompartments> <listOfSpecies> <species metaid="s2" id="s2" name="Nsp4 (+)" compartment="c9" initialAmount="0" charge="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>RNA</celldesigner:class> <celldesigner:rnaReference>rn1</celldesigner:rnaReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s2"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s5" id="s5" name="Nsp4" compartment="c9" initialAmount="0" charge="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Non-structural protein 4 Nsp4 forms a complex with Nsp3 and Nsp6. [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr1</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s5"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:ncbiprotein:BCD58761"/> </rdf:Bag> </bqbiol:isEncodedBy> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:taxonomy:2697049"/> </rdf:Bag> </bqbiol:isEncodedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s24" id="s24" name="IDE" compartment="c9" initialAmount="0" charge="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>UNIPROT: P14735 FUNCTION: Insulin Degrading Enzyme (EC 3.4.24.-). This gene encodes a zinc metallopeptidase that degrades intracellular insulin (DOI:10.1210/mend-4-8-1125 ) Involved in antigen presentation via MHC class I. [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr6</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s24"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:uniprot:P14735"/> </rdf:Bag> </bqbiol:isEncodedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:doi:10.1210%2Fmend-4-8-1125"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s49" id="s49" name="NUP210" compartment="c2" initialAmount="0" charge="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>UNIPROT:Q8TEM1 FUNCTION: Nucleoporin essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as structural integrity. (DOI: 10.1091/mbc.e03-04-0260) </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr7</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s49"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:uniprot:Q8TEM1"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:14517331"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s91" id="s91" name="DNAJC11" compartment="c3" initialAmount="0" charge="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>UNIPROT: Q9NVH1 FUNCTION: Required for mitochondrial inner membrane organization. Seems to function through its association with the MICOS complex and the mitochondrial outer membrane sorting assembly machinery (SAM) complex. </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr11</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s91"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:uniprot:Q9NVH1"/> </rdf:Bag> </bqbiol:isEncodedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:25997101"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s97" id="s97" name="ALG11" compartment="c2" initialAmount="0" charge="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>UNIPROT:Q2TAA5 FUNCTION:Mannosyltransferase involved in the last steps of the synthesis of Man5GlcNAc2-PP-dolichol core oligosaccharide on the cytoplasmic face of the endoplasmic reticulum. Catalyzes the addition of the 4th and 5th mannose residues to the dolichol-linked oligosaccharide chain (DOI:10.1093/hmg/ddq016) Mannosyltransfer ase involved in the synthesis of core oligosaccharide.[PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr12</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s97"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:uniprot:Q2TAA5"/> </rdf:Bag> </bqbiol:isEncodedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:20080937"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s55" id="s55" name="Nsp4_IDE" compartment="c10" initialAmount="0" charge="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>Nsp4_IDE</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s98" id="s98" name="Nsp4_ALG11" compartment="c2" initialAmount="0" charge="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Nsp4 binds to ALG11 [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>Nsp4_ALG11</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s98"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:20080937"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s36" id="s36" name="Nsp6 (+)" compartment="c9" initialAmount="0" charge="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>RNA</celldesigner:class> <celldesigner:rnaReference>rn2</celldesigner:rnaReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s36"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s37" id="s37" name="Nsp6" compartment="c9" initialAmount="0" charge="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>UniProt: P0DTC6 NS6_SARS2 Non-structural protein Nsp6 limits autophagasome expansion. Nsp6 may favor SARS-CoV infection by compromising the ability of autophagosomes to deliver lysosomes for degradation -Complexes with Nsp3 and Nsp4 to form double-membrane vesicles that anchor viral replication complexes. [PMID: 32353859] From SARS-COV-1: Coronavirus nsp6 is a multipass transmembrane protein implicated in the formation of DMVs during SARS-CoV infection (1). Overexpression of nsp6 of IBV, MHV, or SARS-CoV activated the formation of autophagosomes from the ER via an omegasome intermediate (18). However, autophagosomes induced by IBV infection or overexpression of coronavirus nsp6 had smaller diameters compared with those induced by starvation, indicating that nsp6 might also restrict the expansion of autophagosomes (19). [PMID: 31226023] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr3</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s37"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:taxonomy:2697049"/> </rdf:Bag> </bqbiol:isEncodedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s43" id="s43" name="SIGMAR1" compartment="c2" initialAmount="0" charge="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>UNIPROT:Q99720 FUNCTION:Functions in lipid transport from the endoplasmic reticulum and is involved in a wide array of cellular functions probably through regulation of the biogenesis of lipid microdomains at the plasma membrane. (DOI:10.1074/jbc.272.43.27107) Sigma Receptor 1 is an ER chaperone protein that modulates calcium signaling through its interaction with the IP3 receptor. It is targeted by a number of existing drugs including Chloroquine and haloperidol. [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr13</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s43"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:uniprot:Q99720"/> </rdf:Bag> </bqbiol:isEncodedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:doi:10.1074%2Fjbc.272.43.27107"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:10406945"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s70" id="s70" name="TOM complex" compartment="c4" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>TOM complex is made from TOMM 5, 7, 20, 22, 40 and 70.[https://www.genenames.org/data/genegroup/#!/group/1229] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>TOM complex</celldesigner:name> </celldesigner:speciesIdentity> <celldesigner:listOfCatalyzedReactions> <celldesigner:catalyzed reaction="re63"/> </celldesigner:listOfCatalyzedReactions> </celldesigner:extension> </annotation> </species> <species metaid="s112" id="s112" name="TIM complex" compartment="c3" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>[PMID: 27554484] TIM Complex: Involved in the import and insertion of hydrophobic membrane proteins into the mitochondrial inner membrane. Regulates import of transmembrane proteins into the inner mitochondrial membrane. [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>TIM complex</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s213" id="s213" name="V-ATPase" compartment="c2" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>http://www.ebi.ac.uk/interpro/entry/InterPro/IPR008388/ </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>V-ATPase</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s226" id="s226" name="V-ATPase" compartment="c7" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>http://www.ebi.ac.uk/interpro/entry/InterPro/IPR008388/ </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>V-ATPase</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s226"> <bqmodel:is> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:uniprot:Q15904"/> </rdf:Bag> </bqmodel:is> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s247" id="s247" name="V-ATPase:Nsp6" compartment="c7" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Nsp6 binds ATP6AP1 [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>V-ATPase:Nsp6</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s247"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:uniprot:Q15904"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s249" id="s249" name="V-ATPase:Nsp6" compartment="c2" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Nsp6 binds ATP6AP1 [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>V-ATPase:Nsp6</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s250" id="s250" name="TIM complex:Nsp4" compartment="c3" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Tim29 is a novel subunit of the human TIM22 translocase and is involved in complex assembly and stability. [PMID:27554484] Nsp6 binds TIMM9, 10, 10B and 29. [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>TIM complex:Nsp4</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s250"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s252" id="s252" name="IDE" compartment="c10" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>UNIPROT: P14735 FUNCTION: Insulin Degrading Enzyme (EC 3.4.24.-). This gene encodes a zinc metallopeptidase that degrades intracellular insulin (DOI:10.1210/mend-4-8-1125 ) </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr6</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s281" id="s281" name="sa169_degraded" compartment="c9" initialAmount="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>DEGRADED</celldesigner:class> <celldesigner:name>sa169_degraded</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s279" id="s279" name="Nsp3 (+)" compartment="c9" initialAmount="0" charge="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>RNA</celldesigner:class> <celldesigner:rnaReference>rn3</celldesigner:rnaReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s279"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s282" id="s282" name="sa170_degraded" compartment="c9" initialAmount="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>DEGRADED</celldesigner:class> <celldesigner:name>sa170_degraded</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s284" id="s284" name="Nsp3:Nsp4:Nsp6" compartment="c8" initialAmount="0" charge="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Nsp4 forms a complex with Nsp3 and Nsp6. Together, these proteins are predicted to nucleate and anchor viral replication complexes on double-membrane vesicles in the cytoplasm. [PMID: 32353859] From SARS-COV-1: Through similar assays, the region PL2pro−NAB−βSM was found to interact with Nsp4 as well as Nsp12 (Pan et al., 2008). The SARS-CoV PL2pro was further shown to bind ORF7a and Nsp6 by using proteomics analysis (Neuman et al., 2008). [PMID:29128390] From SARS-COV-1: We demonstrated that binding of nsp4 with nsp3 is essential for membrane rearrangement and identified amino acid residues in nsp4 responsible for the interaction with nsp3. (DOI:10.1016/j.virol.2017.07.019) </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>Nsp3:Nsp4:Nsp6</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s284"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:29128390"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:doi:10.1016%2Fj.virol.2017.07.019"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:taxonomy:694009"/> </rdf:Bag> </bqbiol:isEncodedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s283" id="s283" name="sa171_degraded" compartment="c9" initialAmount="0" charge="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>DEGRADED</celldesigner:class> <celldesigner:name>sa171_degraded</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s257" id="s257" name="P-ATPase:Nsp6" compartment="c9" initialAmount="0" charge="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Nsp6 binds ATP13A3 [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>P-ATPase:Nsp6</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s264" id="s264" name="P-ATPase" compartment="c9" initialAmount="0" charge="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>P-ATPases may also exist in organelles, but no evidence found for DMVs. </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>P-ATPase</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s258" id="s258" name="Nsp3" compartment="c8" initialAmount="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr27</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s258"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:taxonomy:2697049"/> </rdf:Bag> </bqbiol:isEncodedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s289" id="s289" name="F-ATPase:Nsp6" compartment="c3" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Nsp6 binds ATP5MG [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>F-ATPase:Nsp6</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s291" id="s291" name="Nsp6:SIGMAR1" compartment="c2" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Nsp6 binds SIGMAR1 [PMID: 32353859] Not sure if the binding happens in the ER, in the cytoplasm or at the nucleus </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>Nsp6:SIGMAR1</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s291"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s292" id="s292" name="Nsp4:NUP210" compartment="c2" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Nsp6 binds NUP210 [PMID: 32353859] Not sure if this binding happens in the ER, in the cytoplasm or at the nuclear membrane </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>innerSurface</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>Nsp4:NUP210</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s293" id="s293" name="Nsp4:IDE" compartment="c9" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Nsp6 binds IDE [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>Nsp4:IDE</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s293"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:taxonomy:10116"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s294" id="s294" name="Nsp4:IDE" compartment="c9" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Nsp6 binds IDE [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>Nsp4:IDE</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s294"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:9830016"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s300" id="s300" name="Nsp4:DNAJC11" compartment="c3" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Nsp6 binds DNAJC11 [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>Nsp4:DNAJC11</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s300"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:25997101"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s301" id="s301" name="Nsp6:SIGMAR1" compartment="c5" initialAmount="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>Nsp6:SIGMAR1</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s302" id="s302" name="Nsp4:NUP210" compartment="c5" initialAmount="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>Nsp4:NUP210</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s302"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:14517331"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s304" id="s304" name="Selinexor" compartment="c9" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>[PMID:32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>DRUG</celldesigner:class> <celldesigner:name>Selinexor</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s304"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s305" id="s305" name="Bafilomycin A1" compartment="c9" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>[PMID:9572882] [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>DRUG</celldesigner:class> <celldesigner:name>Bafilomycin A1</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s306" id="s306" name="NUP210:Selinexor" compartment="c2" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>[PMID:32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>NUP210:Selinexor</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s306"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s309" id="s309" name="SLC6A15" compartment="c9" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>While SLC15A3 was not identified as an interactor of Orf3a, we identified interactions between SARS-CoV-2 proteins and other members of the solute carrier superfamily including SLC25A17 (SARS-CoV-2 Orf9b and Orf9c) and SLC6A15 (SARS-CoV-2 Orf9c, M and Nsp6), although these interactions fall below our scoring thresholds [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr32</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s309"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:uniprot:Q8IY34"/> </rdf:Bag> </bqbiol:isEncodedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s310" id="s310" name="Orf9c" compartment="c9" initialAmount="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr33</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s310"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:taxonomy:2697049"/> </rdf:Bag> </bqbiol:isEncodedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s311" id="s311" name="SLC6A15:Nsp6" compartment="c9" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Nsp6 binds to SLC6A15 [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>SLC6A15:Nsp6</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s311"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s313" id="s313" name="SLC6A15:Orf9c" compartment="c9" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Orf9c binds to SLC6A15 [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>SLC6A15:Orf9c</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s313"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s314" id="s314" name="M" compartment="c9" initialAmount="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr34</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s314"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:taxonomy:2697049"/> </rdf:Bag> </bqbiol:isEncodedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s315" id="s315" name="SLC6A15:M" compartment="c9" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>M binds to SLC6A15 [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>SLC6A15:M</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s315"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s322" id="s322" name="Loratadine" compartment="c9" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>[PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>DRUG</celldesigner:class> <celldesigner:name>Loratadine</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s322"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:123134323"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s323" id="s323" name="SLC6A15:Loratadine" compartment="c9" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>[PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>SLC6A15:Loratadine</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s326" id="s326" name="ATP6AP1:Bafilomycin A1" compartment="c2" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>[PMID:9572882] [PMID:32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>ATP6AP1:Bafilomycin A1</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s344" id="s344" name="Several drugs" compartment="c9" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>SIGMAR interacts with many drugs: BD1008, Carbapentane, Chloroquine, Clemastine, Cloperastine, Dextromethorphan, E-52862, Haloperidol, Hydroxychloroquine, Ifenprodil, Olanzapine, PB28, PD-144418, Pimozide, Progesterone, Rimcazole, RS-PPCC, Siramesine [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>DRUG</celldesigner:class> <celldesigner:name>Several drugs</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s345" id="s345" name="SIGMAR1:Drugs" compartment="c2" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>SIGMAR interacts with many drugs: BD1008, Carbapentane, Chloroquine, Clemastine, Cloperastine, Dextromethorphan, E-52862, Haloperidol, Hydroxychloroquine, Ifenprodil, Olanzapine, PB28, PD-144418, Pimozide, Progesterone, Rimcazole, RS-PPCC, Siramesine [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>SIGMAR1:Drugs</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s345"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s350" id="s350" name="sa5_degraded" compartment="c9" initialAmount="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>DEGRADED</celldesigner:class> <celldesigner:name>sa5_degraded</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s351" id="s351" name="sa2_degraded" compartment="c9" initialAmount="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>DEGRADED</celldesigner:class> <celldesigner:name>sa2_degraded</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s352" id="s352" name="sa3_degraded" compartment="c9" initialAmount="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>DEGRADED</celldesigner:class> <celldesigner:name>sa3_degraded</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s353" id="s353" name="Nsp4" compartment="c4" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Non-structural protein 4 Nsp4 forms a complex with Nsp3 and Nsp6. [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr1</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s353"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:ncbiprotein:BCD58761"/> </rdf:Bag> </bqbiol:isEncodedBy> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:taxonomy:2697049"/> </rdf:Bag> </bqbiol:isEncodedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s355" id="s355" name="Nsp6 (-)" compartment="c9" initialAmount="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>RNA</celldesigner:class> <celldesigner:rnaReference>rn4</celldesigner:rnaReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s355"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s357" id="s357" name="Nsp3 (-)" compartment="c9" initialAmount="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>RNA</celldesigner:class> <celldesigner:rnaReference>rn5</celldesigner:rnaReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s357"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s358" id="s358" name="Nsp4 (-)" compartment="c9" initialAmount="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>RNA</celldesigner:class> <celldesigner:rnaReference>rn6</celldesigner:rnaReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s358"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s384" id="s384" name="P-ATPase" compartment="c9" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>P-ATPases may also exist in organelles, but no evidence found for DMVs. </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>P-ATPase</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s387" id="s387" name="ATP13A3" compartment="c9" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> UNIPROT:Q9H7F0 FUNCTION:Probable cation-transporting ATPase 13A3 </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr5</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s387"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:uniprot:Q9H7F0"/> </rdf:Bag> </bqbiol:isEncodedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s388" id="s388" name="P0" compartment="c9" initialAmount="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>P0</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s389" id="s389" name="P1" compartment="c9" initialAmount="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>P1</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s397" id="s397" name="ATP6AP1" compartment="c2" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> UNIPROT:Q15904 V-Type Proton ATPase Subunit S1 FUNCTION:Accessory subunit of the proton-transporting vacuolar (V)-ATPase protein pump, which is required for luminal acidification of secretory vesicles. Guides the V-type ATPase into specialized subcellular compartments </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr14</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s397"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:uniprot:Q15904"/> </rdf:Bag> </bqbiol:isEncodedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:27231034"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s212" id="s212" name="Plasma membrane organization" compartment="c9" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Rearrengement of plasma membrane GO:0007009 From SARS-COV-1: nsp3, 4, and 6 also induce rearrangement of the cellular membrane to form double-membrane vesicles (DMVs) or spherules (1,77), where the coronavirus replication transcription complex (RTC) is assembled and anchored. [PMID: 31226023] From SARS-COV-1: Together, nsp3, nsp4, and nsp6 have the ability to induce double-membrane vesicles that are similar to those observed in SARS coronavirus-infected cells. [PMID:23943763] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PHENOTYPE</celldesigner:class> <celldesigner:name>Plasma membrane organization</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s212"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0007009"/> </rdf:Bag> </bqbiol:isEncodedBy> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:taxonomy:694009"/> </rdf:Bag> </bqbiol:isEncodedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:31226023"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:23943763"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s398" id="s398" name="NUP210" compartment="c5" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>UNIPROT:Q8TEM1 FUNCTION: Nucleoporin essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as structural integrity. (DOI: 10.1091/mbc.e03-04-0260) </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr7</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s398"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:uniprot:Q8TEM1"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:14517331"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s399" id="s399" name="IDE" compartment="c9" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>UNIPROT: P14735 FUNCTION: Insulin Degrading Enzyme (EC 3.4.24.-). This gene encodes a zinc metallopeptidase that degrades intracellular insulin (DOI:10.1210/mend-4-8-1125 ) Involved in antigen presentation via MHC class I. [PMID: 32353859] In plasma membrane by taxonomyin Rat (Taxonomy: 10116) </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr6</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s399"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:uniprot:P14735"/> </rdf:Bag> </bqbiol:isEncodedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:doi:10.1210%2Fmend-4-8-1125"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:taxonomy:10116"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s400" id="s400" name="SIGMAR1" compartment="c5" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>UNIPROT:Q99720 FUNCTION:Functions in lipid transport from the endoplasmic reticulum and is involved in a wide array of cellular functions probably through regulation of the biogenesis of lipid microdomains at the plasma membrane. (DOI:10.1074/jbc.272.43.27107) Sigma Receptor 1 is an ER chaperone protein that modulates calcium signaling through its interaction with the IP3 receptor. It is targeted by a number of existing drugs including Chloroquine and haloperidol. [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr13</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s400"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:uniprot:Q99720"/> </rdf:Bag> </bqbiol:isEncodedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:doi:10.1074%2Fjbc.272.43.27107"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:10406945"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s401" id="s401" name="SIGMAR1" compartment="c9" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>UNIPROT:Q99720 FUNCTION:Functions in lipid transport from the endoplasmic reticulum and is involved in a wide array of cellular functions probably through regulation of the biogenesis of lipid microdomains at the plasma membrane. (DOI:10.1074/jbc.272.43.27107) Sigma Receptor 1 is an ER chaperone protein that modulates calcium signaling through its interaction with the IP3 receptor. It is targeted by a number of existing drugs including Chloroquine and haloperidol. [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr13</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s401"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:uniprot:Q99720"/> </rdf:Bag> </bqbiol:isEncodedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:doi:10.1074%2Fjbc.272.43.27107"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:10406945"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s402" id="s402" name="Nsp6:SIGMAR1" compartment="c9" initialAmount="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>Nsp6:SIGMAR1</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s402"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:10406945"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s_id_csa1313" id="s_id_csa1313" name="V_minus_type_space_proton_space_ATPase" compartment="c2" initialAmount="0" charge="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Name: lysosomal proton-transporting V-type ATPase complex SemanticZoomLevelVisibility: 5 SemanticZoomLevelTransparency: 4 Charge: 0 A proton-transporting two-sector ATPase complex found in the lysosomal membrane, where it acts as a proton pump to mediate acidification of the lysosomal lumen. </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>V_minus_type_space_proton_space_ATPase</celldesigner:name> </celldesigner:speciesIdentity> <celldesigner:listOfCatalyzedReactions> <celldesigner:catalyzed reaction="re78"/> </celldesigner:listOfCatalyzedReactions> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s_id_csa1313"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0046611"/> </rdf:Bag> </bqbiol:isEncodedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s413" id="s413" name="H_plus_" compartment="c9" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Name: hydron Synonyms: H(+), H+, Hydron SemanticZoomLevelVisibility: 4 SemanticZoomLevelTransparency: 0 </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>ION</celldesigner:class> <celldesigner:name>H_plus_</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s413"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A15378"/> </rdf:Bag> </bqbiol:isEncodedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s406" id="s406" name="Nsp4_ALG11" compartment="c2" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Nsp4 binds to ALG11 [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>Nsp4_ALG11</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s406"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:20080937"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s405" id="s405" name="ALG11" compartment="c2" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>UNIPROT:Q2TAA5 FUNCTION:Mannosyltransferase involved in the last steps of the synthesis of Man5GlcNAc2-PP-dolichol core oligosaccharide on the cytoplasmic face of the endoplasmic reticulum. Catalyzes the addition of the 4th and 5th mannose residues to the dolichol-linked oligosaccharide chain (DOI:10.1093/hmg/ddq016) Mannosyltransfer ase involved in the synthesis of core oligosaccharide.[PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr12</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s405"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:uniprot:Q2TAA5"/> </rdf:Bag> </bqbiol:isEncodedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:20080937"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s419" id="s419" name="H_plus_" compartment="c2" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Name: hydron Synonyms: H(+), H+, Hydron SemanticZoomLevelVisibility: 4 SemanticZoomLevelTransparency: 0 </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>ION</celldesigner:class> <celldesigner:name>H_plus_</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s419"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A15378"/> </rdf:Bag> </bqbiol:isEncodedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s429" id="s429" name="F-ATPase" compartment="c3" initialAmount="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>F-ATPase</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s429"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:uniprot:O75964"/> </rdf:Bag> </bqbiol:isEncodedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s433" id="s433" name="F0" compartment="c3" initialAmount="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>F0</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s434" id="s434" name="F1" compartment="c3" initialAmount="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>F1</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> </annotation> </species> <species metaid="s435" id="s435" name="F-ATPase" compartment="c3" initialAmount="0"> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>COMPLEX</celldesigner:class> <celldesigner:name>F-ATPase</celldesigner:name> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s435"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:uniprot:O75964"/> </rdf:Bag> </bqbiol:isEncodedBy> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="s438" id="s438" name="ATP5MG" compartment="c3" initialAmount="0"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body> UNIPROT:O75964 ATP synthase membrane subunit g </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment> <celldesigner:speciesIdentity> <celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:proteinReference>pr4</celldesigner:proteinReference> </celldesigner:speciesIdentity> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#s438"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:uniprot:O75964"/> </rdf:Bag> </bqbiol:isEncodedBy> </rdf:Description> </rdf:RDF> </annotation> </species> </listOfSpecies> <listOfReactions> <reaction metaid="re1" id="re1" reversible="false"> <annotation> <celldesigner:extension> <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s358" alias="sa220"> <celldesigner:linkAnchor position="NNE"/> </celldesigner:baseReactant> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s2" alias="sa3"> <celldesigner:linkAnchor position="SE"/> </celldesigner:baseProduct> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#re1"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference metaid="CDMT00001" species="s358"> <annotation> <celldesigner:extension> <celldesigner:alias>sa220</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00002" species="s2"> <annotation> <celldesigner:extension> <celldesigner:alias>sa3</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="re2" id="re2" reversible="false"> <annotation> <celldesigner:extension> <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s2" alias="sa3"/> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s5" alias="sa4"/> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#re2"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference metaid="CDMT00003" species="s2"> <annotation> <celldesigner:extension> <celldesigner:alias>sa3</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00004" species="s5"> <annotation> <celldesigner:extension> <celldesigner:alias>sa4</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="re3" id="re3" reversible="false"> <annotation> <celldesigner:extension> <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s5" alias="sa4"/> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s350" alias="sa5"/> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> </annotation> <listOfReactants> <speciesReference metaid="CDMT00005" species="s5"> <annotation> <celldesigner:extension> <celldesigner:alias>sa4</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00006" species="s350"> <annotation> <celldesigner:extension> <celldesigner:alias>sa5</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="re4" id="re4" reversible="false"> <annotation> <celldesigner:extension> <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s2" alias="sa3"/> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s351" alias="sa6"/> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> </annotation> <listOfReactants> <speciesReference metaid="CDMT00007" species="s2"> <annotation> <celldesigner:extension> <celldesigner:alias>sa3</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00008" species="s351"> <annotation> <celldesigner:extension> <celldesigner:alias>sa6</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="re8" id="re6" reversible="false"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Nsp6 binds IDE [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s5" alias="sa4"/> <celldesigner:baseReactant species="s24" alias="sa8"/> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s294" alias="csa2"/> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection arm="0" index="0" value="unknown"/> <celldesigner:lineDirection arm="1" index="0" value="unknown"/> <celldesigner:lineDirection arm="2" index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:editPoints num0="0" num1="0" num2="0" tShapeIndex="0">12.4536235468711,-4.372990353697723</celldesigner:editPoints> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#re8"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:taxonomy:2697049"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference metaid="CDMT00012" species="s5"> <annotation> <celldesigner:extension> <celldesigner:alias>sa4</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> <speciesReference metaid="CDMT00013" species="s24"> <annotation> <celldesigner:extension> <celldesigner:alias>sa8</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00014" species="s294"> <annotation> <celldesigner:extension> <celldesigner:alias>csa2</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="re9" id="re7" reversible="false"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>IDE can be found in cytosol, extracellular region or secreted, mitochondrion, nucleus, peroxisome and plasma Membrane [https://www.uniprot.org/uniprot/P14735#subcellular_location] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s294" alias="csa2"/> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s293" alias="csa4"/> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> </annotation> <listOfReactants> <speciesReference metaid="CDMT00015" species="s294"> <annotation> <celldesigner:extension> <celldesigner:alias>csa2</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00016" species="s293"> <annotation> <celldesigner:extension> <celldesigner:alias>csa4</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="re13" id="re9" reversible="false"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Nsp6 binds NUP210 [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s5" alias="sa4"/> <celldesigner:baseReactant species="s49" alias="sa9"/> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s292" alias="csa14"/> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection arm="0" index="0" value="unknown"/> <celldesigner:lineDirection arm="1" index="0" value="unknown"/> <celldesigner:lineDirection arm="2" index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:editPoints num0="0" num1="0" num2="0" tShapeIndex="0">0.8917243856138661,-0.14849930737262085</celldesigner:editPoints> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#re13"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:taxonomy:2697049"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference metaid="CDMT00019" species="s5"> <annotation> <celldesigner:extension> <celldesigner:alias>sa4</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> <speciesReference metaid="CDMT00020" species="s49"> <annotation> <celldesigner:extension> <celldesigner:alias>sa9</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00021" species="s292"> <annotation> <celldesigner:extension> <celldesigner:alias>csa14</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="re14" id="re10" reversible="false"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>IDE can be found in cytosol, extracellular region or secreted, mitochondrion, nucleus, peroxisome and plasma Membrane [https://www.uniprot.org/uniprot/P14735#subcellular_location] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s294" alias="csa2"/> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s55" alias="csa5"> <celldesigner:linkAnchor position="S"/> </celldesigner:baseProduct> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> </annotation> <listOfReactants> <speciesReference metaid="CDMT00022" species="s294"> <annotation> <celldesigner:extension> <celldesigner:alias>csa2</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00023" species="s55"> <annotation> <celldesigner:extension> <celldesigner:alias>csa5</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="re21" id="re16" reversible="false"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Nsp6 binds DNAJC11 [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s5" alias="sa4"/> <celldesigner:baseReactant species="s91" alias="sa13"/> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s300" alias="csa12"/> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection arm="0" index="0" value="unknown"/> <celldesigner:lineDirection arm="1" index="0" value="unknown"/> <celldesigner:lineDirection arm="2" index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:editPoints num0="0" num1="0" num2="0" tShapeIndex="0">0.6321848020534473,0.017033522594620543</celldesigner:editPoints> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#re21"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:taxonomy:2697049"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference metaid="CDMT00037" species="s5"> <annotation> <celldesigner:extension> <celldesigner:alias>sa4</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> <speciesReference metaid="CDMT00038" species="s91"> <annotation> <celldesigner:extension> <celldesigner:alias>sa13</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00039" species="s300"> <annotation> <celldesigner:extension> <celldesigner:alias>csa12</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="re22" id="re17" reversible="false"> <annotation> <celldesigner:extension> <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s292" alias="csa14"> <celldesigner:linkAnchor position="S"/> </celldesigner:baseReactant> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s302" alias="csa13"> <celldesigner:linkAnchor position="N"/> </celldesigner:baseProduct> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#re22"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:14517331"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference metaid="CDMT00040" species="s292"> <annotation> <celldesigner:extension> <celldesigner:alias>csa14</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00041" species="s302"> <annotation> <celldesigner:extension> <celldesigner:alias>csa13</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="re23" id="re18" reversible="false"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>[PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s5" alias="sa4"/> <celldesigner:baseReactant species="s97" alias="sa14"/> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s98" alias="csa15"/> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection arm="0" index="0" value="unknown"/> <celldesigner:lineDirection arm="1" index="0" value="unknown"/> <celldesigner:lineDirection arm="2" index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:editPoints num0="0" num1="0" num2="0" tShapeIndex="0">1.2323452089565818,-0.35651044027438217</celldesigner:editPoints> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#re23"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:taxonomy:2697049"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference metaid="CDMT00042" species="s5"> <annotation> <celldesigner:extension> <celldesigner:alias>sa4</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> <speciesReference metaid="CDMT00043" species="s97"> <annotation> <celldesigner:extension> <celldesigner:alias>sa14</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00044" species="s98"> <annotation> <celldesigner:extension> <celldesigner:alias>csa15</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="re24" id="re19" reversible="false"> <annotation> <celldesigner:extension> <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s2" alias="sa3"> <celldesigner:linkAnchor position="SSW"/> </celldesigner:baseReactant> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s358" alias="sa220"> <celldesigner:linkAnchor position="NW"/> </celldesigner:baseProduct> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#re24"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference metaid="CDMT00045" species="s2"> <annotation> <celldesigner:extension> <celldesigner:alias>sa3</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00046" species="s358"> <annotation> <celldesigner:extension> <celldesigner:alias>sa220</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="re25" id="re20" reversible="false"> <annotation> <celldesigner:extension> <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s358" alias="sa220"/> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s352" alias="sa16"/> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> </annotation> <listOfReactants> <speciesReference metaid="CDMT00047" species="s358"> <annotation> <celldesigner:extension> <celldesigner:alias>sa220</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00048" species="s352"> <annotation> <celldesigner:extension> <celldesigner:alias>sa16</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="CDMT00054" id="re21" reversible="false"> <annotation> <celldesigner:extension> <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s355" alias="sa218"> <celldesigner:linkAnchor position="NE"/> </celldesigner:baseReactant> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s36" alias="sa47"> <celldesigner:linkAnchor position="NW"/> </celldesigner:baseProduct> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> <rdf:RDF 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metaid="CDMT00057" id="re22" reversible="false"> <annotation> <celldesigner:extension> <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s36" alias="sa47"/> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s37" alias="sa48"/> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#CDMT00057"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference metaid="CDMT00058" species="s36"> <annotation> <celldesigner:extension> <celldesigner:alias>sa47</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00059" species="s37"> <annotation> <celldesigner:extension> <celldesigner:alias>sa48</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="CDMT00060" id="re23" reversible="false"> <annotation> <celldesigner:extension> <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s37" alias="sa48"/> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s350" alias="sa49"/> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> </annotation> <listOfReactants> <speciesReference metaid="CDMT00061" species="s37"> <annotation> <celldesigner:extension> <celldesigner:alias>sa48</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00062" species="s350"> <annotation> <celldesigner:extension> <celldesigner:alias>sa49</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="CDMT00063" id="re24" reversible="false"> <annotation> <celldesigner:extension> <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s36" alias="sa47"/> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s351" alias="sa50"/> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> </annotation> <listOfReactants> <speciesReference metaid="CDMT00064" species="s36"> <annotation> <celldesigner:extension> <celldesigner:alias>sa47</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00065" species="s351"> <annotation> <celldesigner:extension> <celldesigner:alias>sa50</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="CDMT00066" id="re25" reversible="false"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Nsp6 binds ATP5MG [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s37" alias="sa48"/> <celldesigner:baseReactant species="s429" alias="csa42"/> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s289" alias="csa43"/> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection arm="0" index="0" value="unknown"/> <celldesigner:lineDirection arm="1" index="0" value="unknown"/> <celldesigner:lineDirection arm="2" index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:editPoints num0="0" num1="0" num2="0" tShapeIndex="0">-59.43541835905478,52.11546942090979</celldesigner:editPoints> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#CDMT00066"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:taxonomy:2697049"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference metaid="CDMT00067" species="s37"> <annotation> <celldesigner:extension> <celldesigner:alias>sa48</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> <speciesReference metaid="CDMT00068" species="s429"> <annotation> <celldesigner:extension> <celldesigner:alias>csa42</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00069" species="s289"> <annotation> <celldesigner:extension> <celldesigner:alias>csa43</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="re7" id="re26" reversible="false"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Nsp6 binds ATP13A3 [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s37" alias="sa48"/> <celldesigner:baseReactant species="s264" alias="csa41"/> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s257" alias="csa40"/> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection arm="0" index="0" value="unknown"/> <celldesigner:lineDirection arm="1" index="0" value="unknown"/> <celldesigner:lineDirection arm="2" index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:editPoints num0="0" num1="0" num2="0" tShapeIndex="0">1.8185065380638896,-1.5071447155197912</celldesigner:editPoints> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#re7"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:taxonomy:2697049"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference metaid="CDMT00070" species="s37"> <annotation> <celldesigner:extension> <celldesigner:alias>sa48</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> <speciesReference metaid="CDMT00071" species="s264"> <annotation> <celldesigner:extension> <celldesigner:alias>csa41</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00072" species="s257"> <annotation> <celldesigner:extension> <celldesigner:alias>csa40</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="re27" id="re27" reversible="false"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Nsp6 binds SIGMAR1 [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s37" alias="sa48"/> <celldesigner:baseReactant species="s43" alias="sa53"/> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s291" alias="csa18"/> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection arm="0" index="0" value="unknown"/> <celldesigner:lineDirection arm="1" index="0" value="unknown"/> <celldesigner:lineDirection arm="2" index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:editPoints num0="0" num1="0" num2="0" tShapeIndex="0">0.12370442720793662,0.8013710872245996</celldesigner:editPoints> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#re27"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:taxonomy:2697049"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference metaid="CDMT00073" species="s37"> <annotation> <celldesigner:extension> <celldesigner:alias>sa48</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> <speciesReference metaid="CDMT00074" species="s43"> <annotation> <celldesigner:extension> <celldesigner:alias>sa53</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00075" species="s291"> <annotation> <celldesigner:extension> <celldesigner:alias>csa18</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="re28" id="re28" reversible="false"> <annotation> <celldesigner:extension> <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s291" alias="csa18"> <celldesigner:linkAnchor position="S"/> </celldesigner:baseReactant> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s301" alias="csa19"> <celldesigner:linkAnchor position="N"/> </celldesigner:baseProduct> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#re28"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:10406945"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference metaid="CDMT00076" species="s291"> <annotation> <celldesigner:extension> <celldesigner:alias>csa18</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00077" species="s301"> <annotation> <celldesigner:extension> <celldesigner:alias>csa19</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="re31" id="re31" reversible="false"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title/> </head> <body>Nsp6 binds ATP6AP1 [PMID: 32353859] </body> </html> </notes> <annotation> <celldesigner:extension> <celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s37" alias="sa48"/> <celldesigner:baseReactant species="s213" alias="csa30"/> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s249" alias="csa32"/> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection arm="0" index="0" value="unknown"/> <celldesigner:lineDirection arm="1" index="0" value="unknown"/> <celldesigner:lineDirection arm="2" index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:editPoints num0="0" num1="0" num2="0" tShapeIndex="0">0.9289681281145725,-0.035911008067335715</celldesigner:editPoints> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#re31"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:taxonomy:2697049"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference metaid="CDMT00084" species="s37"> <annotation> <celldesigner:extension> <celldesigner:alias>sa48</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> <speciesReference metaid="CDMT00085" species="s213"> <annotation> <celldesigner:extension> <celldesigner:alias>csa30</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00086" species="s249"> <annotation> <celldesigner:extension> <celldesigner:alias>csa32</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="re32" id="re32" reversible="false"> <annotation> <celldesigner:extension> <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType> <celldesigner:baseReactants> <celldesigner:baseReactant species="s36" alias="sa47"> <celldesigner:linkAnchor position="SW"/> </celldesigner:baseReactant> </celldesigner:baseReactants> <celldesigner:baseProducts> <celldesigner:baseProduct species="s355" alias="sa218"> <celldesigner:linkAnchor position="SE"/> </celldesigner:baseProduct> </celldesigner:baseProducts> <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0"> <celldesigner:listOfLineDirection> <celldesigner:lineDirection index="0" value="unknown"/> </celldesigner:listOfLineDirection> </celldesigner:connectScheme> <celldesigner:line width="1.0" color="ff000000"/> </celldesigner:extension> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#re32"> <bqbiol:isDescribedBy> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:32353859"/> </rdf:Bag> </bqbiol:isDescribedBy> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference metaid="CDMT00087" species="s36"> <annotation> <celldesigner:extension> <celldesigner:alias>sa47</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfReactants> <listOfProducts> <speciesReference metaid="CDMT00088" species="s355"> <annotation> <celldesigner:extension> <celldesigner:alias>sa218</celldesigner:alias> </celldesigner:extension> </annotation> </speciesReference> </listOfProducts> </reaction> <reaction metaid="re33" id="re33" reversible="false"> <annotation> <celldesigner:extension> 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