View source for 9eab


==Seneca valley virus Altered particle at physiological condition (A-particle[P])==
<StructureSection load='9eab' size='340' side='right'caption='[[9eab]], [[Resolution|resolution]] 3.39&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9eab]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Seneca_Valley_virus_USA/SSV-001 Seneca Valley virus USA/SSV-001]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9EAB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9EAB FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.39&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9eab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9eab OCA], [https://pdbe.org/9eab PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9eab RCSB], [https://www.ebi.ac.uk/pdbsum/9eab PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9eab ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/POLG_SVV1 POLG_SVV1] Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3 (PubMed:18940610). Together they form an icosahedral capsid composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 325 Angstroms (Probable). VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3 (By similarity). All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll (By similarity). VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes (PubMed:18940610). Binds the host receptor ANTXR1 for attachment and uncoating (entry) (PubMed:30381454, PubMed:30514821).[UniProtKB:P12296]<ref>PMID:18940610</ref> <ref>PMID:30381454</ref> <ref>PMID:30514821</ref> <ref>PMID:18420805</ref>   Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3 (PubMed:18940610). Together they form an icosahedral capsid composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 270 Angstroms (Probable). VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3 (By similarity). All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll (By similarity). VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes (PubMed:18940610). Binds the host receptor ANTXR1 for attachment and uncoating (entry) (PubMed:30381454, PubMed:30514821).[UniProtKB:P12296]<ref>PMID:18940610</ref> <ref>PMID:30381454</ref> <ref>PMID:30514821</ref> <ref>PMID:18420805</ref>   Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3 (Probable). Together they form an icosahedral capsid composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 270 Angstroms (Probable). VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll (By similarity). VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes (By similarity). Vp3 also seems to be involved in the binding to host receptor ANTXR1 for attachment and uncoating (entry) (PubMed:30381454).[UniProtKB:P12296]<ref>PMID:30381454</ref> <ref>PMID:18420805</ref>   Lies on the inner surface of the capsid shell (PubMed:18940610). After binding to the host receptor, the capsid undergoes conformational changes (By similarity). Capsid protein VP4 is released, capsid protein VP1 N-terminus is externalized, and together, they shape a pore in the host membrane through which the viral genome is translocated into the host cell cytoplasm (By similarity). After genome has been released, the channel shrinks (By similarity).[UniProtKB:P12296]<ref>PMID:18940610</ref>   VP0 precursor is a component of immature procapsids.[UniProtKB:P08617]  Mediates self-processing of the polyprotein by a translational effect termed 'ribosome skipping'. Mechanistically, 2A-mediated cleavage occurs between the C-terminal glycine and the proline of the downstream protein 2B.[UniProtKB:P03305]  Plays an essential role in the virus replication cycle by acting as a viroporin. Creates a pore in the host endoplasmic reticulum and as a consequence releases Ca2+ in the cytoplasm of infected cell. In turn, high levels of cytoplasmic calcium may trigger membrane trafficking and transport of viral ER-associated proteins to viroplasms, sites of viral genome replication.[UniProtKB:P03305]  Associates with and induces structural rearrangements of intracellular membranes.[UniProtKB:P03305]  Covalently linked to the 5'-end of both the positive-strand and negative-strand genomic RNAs. Acts as a genome-linked replication primer.[UniProtKB:P03305]  Cysteine protease that generates mature viral proteins from the precursor polyprotein (By similarity). Inactivates crucial host adapter molecules in order to suppress antiviral type-I interferon (type-I IFN) and NF-kappaB production to escape host antiviral innate immune responses (PubMed:28566380, PubMed:29427864, PubMed:30408499). Deubiquitinase that acts on both lysine-48- and lysine-63-linked polyubiquitin chains and inhibits the ubiquitination of the ATP-dependent RNA helicase RIGI, TANK-binding kinase 1 (TBK1), and TNF receptor-associated factor 3 (TRAF3), thereby blocking the expression of IFN-beta and IFN stimulated gene 54 (ISG54) (PubMed:30408499). Induces host IRF3 and IRF7 degradation thereby suppressing IRF3- and IRF7-induced type-I IFN production (PubMed:29427864). Also decreases host IRF3 phosphorylation leading to negligible IRF3 activation (PubMed:29427864). Cleaves host MAVS, TRIF and TANK, which are then unable to regulate pattern recognition receptor (PRR)-mediated type-I IFN production (PubMed:28566380). Inhibits the integrated stress response (ISR) in the infected cell by disrupting eIF4GI-G3BP1 interaction (PubMed:33133097). Stress granule formation is thus inhibited (PubMed:33133097).[UniProtKB:P12296]<ref>PMID:28566380</ref> <ref>PMID:29427864</ref> <ref>PMID:30408499</ref> <ref>PMID:33133097</ref>   Replicates the genomic and antigenomic RNAs by recognizing replications specific signals (By similarity). Performs VPg uridylylation (By similarity).[UniProtKB:P12296]
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Seneca Valley virus USA/SSV-001]]
[[Category: Bostina M]]
[[Category: Kumaran R]]