Nsp4_Nsp6_proteins_stable.xml 443 KB
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<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
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<model metaid="Nsp4_Nsp6" id="Nsp4_Nsp6">
<notes>
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<p> Authors: Arnau Montagud (arnau.montagud@bsc.es) and Miguel Ponce de León (miguel.ponce@bsc.es) from Barcelona Supercomputing Center</p>
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</html>
</notes>
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<annotation>
<celldesigner:extension>
<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
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<celldesigner:modelDisplay sizeX="3200" sizeY="2000"/>
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<celldesigner:listOfIncludedSpecies>
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<celldesigner:species id="s145" name="TOMM70">
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UNIPROT:O94826
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<celldesigner:complexSpecies>s70</celldesigner:complexSpecies>
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<celldesigner:species id="s94" name="Nsp4">
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<celldesigner:speciesIdentity>
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<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
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</celldesigner:speciesIdentity>
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<celldesigner:species id="s13" name="Nsp4">
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<celldesigner:speciesIdentity>
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<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
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</celldesigner:speciesIdentity>
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<celldesigner:species id="s14" name="NUP210">
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<celldesigner:speciesIdentity>
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<celldesigner:proteinReference>pr7</celldesigner:proteinReference>
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</celldesigner:speciesIdentity>
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<celldesigner:species id="s18" name="Nsp4">
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<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
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<celldesigner:species id="s52" name="Nsp6">
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<celldesigner:proteinReference>pr6</celldesigner:proteinReference>
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<celldesigner:complexSpecies>s291</celldesigner:complexSpecies>
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UNIPROT:Q8N4H5
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<celldesigner:complexSpecies>s70</celldesigner:complexSpecies>
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UNIPROT:Q9P0U1
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<celldesigner:complexSpecies>s70</celldesigner:complexSpecies>
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<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr20</celldesigner:proteinReference>
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<celldesigner:species id="s142" name="TOMM20">
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UNIPROT:Q15388
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<celldesigner:species id="s143" name="TOMM22">
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UNIPROT:Q9NS69
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<celldesigner:class>PROTEIN</celldesigner:class>
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<celldesigner:proteinReference>pr22</celldesigner:proteinReference>
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<celldesigner:species id="s144" name="TOMM40">
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<body>
UNIPROT:O96008
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</html>
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<celldesigner:proteinReference>pr23</celldesigner:proteinReference>
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<celldesigner:species id="s176" name="TIMM29">
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<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.
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</celldesigner:notes>
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<celldesigner:complexSpecies>s112</celldesigner:complexSpecies>
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<celldesigner:class>PROTEIN</celldesigner:class>
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<celldesigner:proteinReference>pr8</celldesigner:proteinReference>
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<celldesigner:species id="s177" name="TIMM22">
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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).
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<celldesigner:proteinReference>pr15</celldesigner:proteinReference>
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<celldesigner:species id="s178" name="TIMM10B">
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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.
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<celldesigner:proteinReference>pr10</celldesigner:proteinReference>
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UNIPROT:Q9Y5J7
FUNCTION:Mitochondrial intermembrane chaperone that participates in the import and insertion of multi-pass transmembrane proteins into the mitochondrial inner membrane.
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<celldesigner:proteinReference>pr2</celldesigner:proteinReference>
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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. Acts as a chaperone-like protein that protects the hydrophobic precursors from aggregation and guide them through the mitochondrial intermembrane space.
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<celldesigner:class>PROTEIN</celldesigner:class>
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<celldesigner:proteinReference>pr9</celldesigner:proteinReference>
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<celldesigner:species id="s203" name="TIMM29">
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<celldesigner:proteinReference>pr8</celldesigner:proteinReference>
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<celldesigner:species id="s204" name="TIMM22">
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<celldesigner:proteinReference>pr15</celldesigner:proteinReference>
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<celldesigner:species id="s205" name="TIMM10B">
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<celldesigner:annotation>
481
<celldesigner:complexSpecies>s250</celldesigner:complexSpecies>
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<celldesigner:proteinReference>pr10</celldesigner:proteinReference>
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<celldesigner:species id="s206" name="TIMM9">
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<celldesigner:complexSpecies>s250</celldesigner:complexSpecies>
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<celldesigner:class>PROTEIN</celldesigner:class>
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<celldesigner:proteinReference>pr2</celldesigner:proteinReference>
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</celldesigner:annotation>
</celldesigner:species>
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<celldesigner:species id="s207" name="TIMM10">
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</celldesigner:notes>
<celldesigner:annotation>
515
<celldesigner:complexSpecies>s250</celldesigner:complexSpecies>
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<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
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<celldesigner:proteinReference>pr9</celldesigner:proteinReference>
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</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
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<celldesigner:species id="s230" name="ATP6AP1">
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<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>
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</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>
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<body>
V-Type Proton ATPase Subunit S1
</body>
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</celldesigner:notes>
<celldesigner:annotation>
555
<celldesigner:complexSpecies>s249</celldesigner:complexSpecies>
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<celldesigner:class>PROTEIN</celldesigner:class>
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<celldesigner:proteinReference>pr14</celldesigner:proteinReference>
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</celldesigner:annotation>
</celldesigner:species>
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<celldesigner:species id="s233" name="Nsp6">
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<celldesigner:annotation>
572
<celldesigner:complexSpecies>s249</celldesigner:complexSpecies>
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<celldesigner:class>PROTEIN</celldesigner:class>
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<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
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</celldesigner:species>
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<celldesigner:species id="s238" name="ATP6AP1">
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<html xmlns="http://www.w3.org/1999/xhtml">
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<body>
V-Type Proton ATPase Subunit S1
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</celldesigner:notes>
<celldesigner:annotation>
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<celldesigner:complexSpecies>s247</celldesigner:complexSpecies>
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<celldesigner:proteinReference>pr14</celldesigner:proteinReference>
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<celldesigner:species id="s239" name="Nsp6">
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<celldesigner:annotation>
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<celldesigner:complexSpecies>s247</celldesigner:complexSpecies>
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<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
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<celldesigner:species id="s285" name="Nsp3">
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<celldesigner:annotation>
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<celldesigner:complexSpecies>s284</celldesigner:complexSpecies>
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<celldesigner:proteinReference>pr27</celldesigner:proteinReference>
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<celldesigner:species id="s286" name="Nsp4">
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<celldesigner:complexSpecies>s284</celldesigner:complexSpecies>
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<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
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<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
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</celldesigner:species>
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<celldesigner:species id="s288" name="Nsp6">
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<celldesigner:annotation>
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<celldesigner:complexSpecies>s284</celldesigner:complexSpecies>
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<celldesigner:class>PROTEIN</celldesigner:class>
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<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
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</celldesigner:annotation>
</celldesigner:species>
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<celldesigner:species id="s298" name="Nsp6">
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</celldesigner:notes>
<celldesigner:annotation>
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<celldesigner:complexSpecies>s257</celldesigner:complexSpecies>
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<celldesigner:speciesIdentity>
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<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
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</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
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<celldesigner:species id="s299" name="ATP13A3">
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</celldesigner:notes>
<celldesigner:annotation>
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<celldesigner:complexSpecies>s257</celldesigner:complexSpecies>
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<celldesigner:speciesIdentity>
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<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr5</celldesigner:proteinReference>
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</celldesigner:annotation>
</celldesigner:species>
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<celldesigner:species id="s295" name="ATP13A3">
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UNIPROT:Q9H7F0
FUNCTION:Probable cation-transporting ATPase 13A3
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</celldesigner:notes>
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<celldesigner:complexSpecies>s264</celldesigner:complexSpecies>
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<celldesigner:proteinReference>pr5</celldesigner:proteinReference>
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<celldesigner:species id="s307" name="NUP210">
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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)
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<celldesigner:complexSpecies>s306</celldesigner:complexSpecies>
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<celldesigner:proteinReference>pr7</celldesigner:proteinReference>
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<celldesigner:species id="s308" name="Selinexor">
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[PMID:32353859]
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</celldesigner:notes>
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<celldesigner:complexSpecies>s306</celldesigner:complexSpecies>
<celldesigner:speciesIdentity>
<celldesigner:class>DRUG</celldesigner:class>
<celldesigner:name>Selinexor</celldesigner:name>
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<celldesigner:species id="s316" name="SLC6A15">
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<celldesigner:annotation>
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<celldesigner:complexSpecies>s315</celldesigner:complexSpecies>
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<celldesigner:class>PROTEIN</celldesigner:class>
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<celldesigner:proteinReference>pr32</celldesigner:proteinReference>
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<celldesigner:annotation>
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<celldesigner:complexSpecies>s313</celldesigner:complexSpecies>
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<celldesigner:class>PROTEIN</celldesigner:class>
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<celldesigner:proteinReference>pr32</celldesigner:proteinReference>
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</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
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<celldesigner:species id="s318" name="SLC6A15">
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</celldesigner:notes>
<celldesigner:annotation>
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<celldesigner:complexSpecies>s311</celldesigner:complexSpecies>
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<celldesigner:class>PROTEIN</celldesigner:class>
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<celldesigner:proteinReference>pr32</celldesigner:proteinReference>
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</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
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<celldesigner:species id="s319" name="Nsp6">
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<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]
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<celldesigner:complexSpecies>s311</celldesigner:complexSpecies>
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<celldesigner:class>PROTEIN</celldesigner:class>
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<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
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</celldesigner:annotation>
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<celldesigner:species id="s320" name="Orf9c">
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<celldesigner:complexSpecies>s313</celldesigner:complexSpecies>
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<celldesigner:class>PROTEIN</celldesigner:class>
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<celldesigner:proteinReference>pr33</celldesigner:proteinReference>
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</celldesigner:species>
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<celldesigner:species id="s321" name="M">
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<celldesigner:complexSpecies>s315</celldesigner:complexSpecies>
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<celldesigner:class>PROTEIN</celldesigner:class>
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<celldesigner:proteinReference>pr34</celldesigner:proteinReference>
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<celldesigner:species id="s324" name="SLC6A15">
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<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]
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</celldesigner:notes>
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<celldesigner:complexSpecies>s323</celldesigner:complexSpecies>
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<celldesigner:class>PROTEIN</celldesigner:class>
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<celldesigner:proteinReference>pr32</celldesigner:proteinReference>
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</celldesigner:annotation>
</celldesigner:species>
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<celldesigner:species id="s335" name="Bafilomycin A1">
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<body>
Gordon 
[PMID:9572882]
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</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">
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<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]
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</celldesigner:notes>
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<celldesigner:class>PROTEIN</celldesigner:class>
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<celldesigner:proteinReference>pr14</celldesigner:proteinReference>
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</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
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<body>
UNIPROT:Q15904
V-Type Proton ATPase Subunit S1
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</celldesigner:notes>
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<celldesigner:proteinReference>pr14</celldesigner:proteinReference>
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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]
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959
</html>
</celldesigner:notes>
<celldesigner:annotation>
960
<celldesigner:complexSpecies>s345</celldesigner:complexSpecies>
961
962
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
963
964
965
966
967
968
969
970
971
972
973
974
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976
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978
979
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981
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1000
<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>
<celldesigner:name>Several drugs</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
<celldesigner:species id="s349" name="Loratadine">
<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body>
[PMID: 32353859]
</body>
</html>
</celldesigner:notes>
<celldesigner:annotation>
<celldesigner:complexSpecies>s323</celldesigner:complexSpecies>
<celldesigner:speciesIdentity>
<celldesigner:class>DRUG</celldesigner:class>
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