3cji

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{{Seed}}
 
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[[Image:3cji.jpg|left|200px]]
 
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==Structure of Seneca Valley Virus-001==
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The line below this paragraph, containing "STRUCTURE_3cji", creates the "Structure Box" on the page.
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<StructureSection load='3cji' size='340' side='right'caption='[[3cji]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3cji]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Senecavirus_A Senecavirus A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CJI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CJI FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
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<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>
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{{STRUCTURE_3cji| PDB=3cji | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3cji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cji OCA], [https://pdbe.org/3cji PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cji RCSB], [https://www.ebi.ac.uk/pdbsum/3cji PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cji ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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).[UniProtKB:P12296]<ref>PMID:18940610</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).[UniProtKB:P12296]<ref>PMID:18940610</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 (PubMed:18420805). 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).[UniProtKB:P12296]<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 reticulum endoplasmic 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:30408499, PubMed:29427864, PubMed:28566380). 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).[UniProtKB:P12296]<ref>PMID:28566380</ref> <ref>PMID:29427864</ref> <ref>PMID:30408499</ref> Replicates the genomic and antigenomic RNAs by recognizing replications specific signals (By similarity). Performs VPg uridylylation (By similarity).[UniProtKB:P12296]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cj/3cji_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3cji ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The crystal structure of Seneca Valley Virus-001 (SVV-001), the representative member of a new genus, Senecavirus, is reported at 2.3A resolution. SVV-001 is the first naturally occurring nonpathogenic picornavirus shown to mediate selective cytotoxicity towards tumor cells with neuroendocrine cancer features. The nonsegmented (+) ssRNA genome of SVV-001 shares closest sequence similarity with the genomes of the members of Cardiovirus. The overall tertiary structure of VP1-VP4 subunits is conserved with the exception of loops, especially those of VP1 that show large deviations relative to the members of the cardioviruses. The surface loops of VP1 and VP2 are predicted to mediate cell tropism of SVV-001. In addition, the organization of the packaged nucleic acid density indicates that certain regions of VP2 and VP4 interact closely with the packaged nucleic acid.
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===Structure of Seneca Valley Virus-001===
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Structure of Seneca Valley Virus-001: an oncolytic picornavirus representing a new genus.,Venkataraman S, Reddy SP, Loo J, Idamakanti N, Hallenbeck PL, Reddy VS Structure. 2008 Oct 8;16(10):1555-61. PMID:18940610<ref>PMID:18940610</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_18940610}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3cji" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 18940610 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18940610}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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3CJI is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Seneca_valley_virus Seneca valley virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CJI OCA].
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[[Category: Senecavirus A]]
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[[Category: Reddy VS]]
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==Reference==
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[[Category: Venkataraman S]]
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Structure of Seneca Valley Virus-001: an oncolytic picornavirus representing a new genus., Venkataraman S, Reddy SP, Loo J, Idamakanti N, Hallenbeck PL, Reddy VS, Structure. 2008 Oct 8;16(10):1555-61. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18940610 18940610]
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[[Category: Seneca valley virus]]
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[[Category: Reddy, V S.]]
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[[Category: Venkataraman, S.]]
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[[Category: Atp-binding]]
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[[Category: Cytoplasm]]
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[[Category: Cytoplasmic vesicle]]
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[[Category: Helicase]]
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[[Category: Hydrolase]]
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[[Category: Icosahedral virus]]
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[[Category: Membrane]]
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[[Category: Nucleotide-binding]]
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[[Category: Nucleotidyltransferase]]
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[[Category: Phosphoprotein]]
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[[Category: Protease]]
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[[Category: Rna replication]]
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[[Category: Rna-binding]]
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[[Category: Rna-directed rna polymerase]]
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[[Category: Thiol protease]]
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[[Category: Transferase]]
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[[Category: Virion]]
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[[Category: Virus]]
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[[Category: Virus capsid protein structure]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 17 13:42:36 2008''
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Current revision

Structure of Seneca Valley Virus-001

PDB ID 3cji

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