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| | <SX load='4v7q' size='340' side='right' viewer='molstar' caption='[[4v7q]], [[Resolution|resolution]] 3.80Å' scene=''> | | <SX load='4v7q' size='340' side='right' viewer='molstar' caption='[[4v7q]], [[Resolution|resolution]] 3.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4v7q]] is a 31 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Rotrh Rotrh]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3iyu 3iyu] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3n09 3n09]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V7Q OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=4V7Q FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4v7q]] is a 31 chain structure with sequence from [https://en.wikipedia.org/wiki/Simian_rotavirus_A_strain_RRV Simian rotavirus A strain RRV]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3iyu 3iyu] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3n09 3n09]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V7Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V7Q FirstGlance]. <br> |
| | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Rotavirus ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=444185 ROTRH])</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=4v7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v7q OCA], [https://pdbe.org/4v7q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v7q RCSB], [https://www.ebi.ac.uk/pdbsum/4v7q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v7q ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=4v7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v7q OCA], [http://pdbe.org/4v7q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4v7q RCSB], [http://www.ebi.ac.uk/pdbsum/4v7q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4v7q ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/C3RX20_9REOV C3RX20_9REOV]] Outer capsid protein VP5*: forms the spike "foot" and "body". Acts as a membrane permeabilization protein that mediates release of viral particles from endosomal compartments into the cytoplasm. In integrin-dependent strains, VP5* targets the integrin heterodimer ITGA2/ITGB1 for cell attachment (By similarity).[SAAS:SAAS000416_004_050839] VP8* forms the head of the spikes. It is the viral hemagglutinin and an important target of neutralizing antibodies. In sialic acid-dependent strains, VP8* binds to host cell sialic acid, most probably a ganglioside, providing the initial contact (By similarity). [[http://www.uniprot.org/uniprot/VP6_ROTRH VP6_ROTRH]] Intermediate capsid protein that self assembles to form an icosahedral capsid with a T=13 symmetry, which consists of 230 trimers of VP6, with channels at each of its five-fold vertices. This capsid constitutes the middle concentric layer of the viral mature particle. The innermost VP2 capsid and the intermediate VP6 capsid remain intact following cell entry to protect the dsRNA from degradation and to prevent unfavorable antiviral responses in the host cell during all the replication cycle of the virus. Nacent transcripts are transcribed within the structural confines of this double-layered particle (DLP) and are extruded through the channels at the five-fold axes. VP6 is required for the transcription activity of the DLP (By similarity). | + | [https://www.uniprot.org/uniprot/B3F2X3_ROTRH B3F2X3_ROTRH] Inner capsid protein that self-assembles to form an icosahedral capsid with a T=2 symmetry, which consists of 120 copies of VP2, with channels at each of its five-fold vertices. This capsid constitutes the innermost concentric layer of the viral mature particle. It encapsidates the polymerase VP1, the capping enzyme VP3 and the genomic dsRNA, thereby defining the core. The innermost VP2 capsid and the intermediate VP6 capsid remain intact following cell entry to protect the dsRNA from degradation and to prevent unfavorable antiviral responses in the host cell during all the replication cycle of the virus. Nascent transcripts are transcribed within the structural confines of this double-layered particle (DLP) and are extruded through the channels formed by VP2 N-termini. VP2 is required for the replicase activity of VP1 polymerase. Probably recruits a copy of a VP1-VP3 complex, potentially along with a segment of plus-strand RNA, as a decamer of VP2 assembles. May activate the autoinhibited VP1/RNA complex to coordinate packaging and genome replication.[RuleBase:RU363125] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </SX> | | </SX> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Rotrh]] | + | [[Category: Simian rotavirus A strain RRV]] |
| - | [[Category: Chen, J Z]] | + | [[Category: Chen JZ]] |
| - | [[Category: Dormitzer, P R]] | + | [[Category: Dormitzer PR]] |
| - | [[Category: Grigorieff, N]] | + | [[Category: Grigorieff N]] |
| - | [[Category: Harrison, S C]] | + | [[Category: Harrison SC]] |
| - | [[Category: Settembre, E C]] | + | [[Category: Settembre EC]] |
| - | [[Category: De novo]]
| + | |
| - | [[Category: Dlp]]
| + | |
| - | [[Category: Double layered particle]]
| + | |
| - | [[Category: Icosahedral virus]]
| + | |
| - | [[Category: Infectious]]
| + | |
| - | [[Category: Near atomic resolution]]
| + | |
| - | [[Category: Rotavirus]]
| + | |
| - | [[Category: Triple layered particle]]
| + | |
| - | [[Category: Virus]]
| + | |
| - | [[Category: Vp2]]
| + | |
| - | [[Category: Vp4]]
| + | |
| - | [[Category: Vp6]]
| + | |
| - | [[Category: Vp7]]
| + | |
| Structural highlights
Function
B3F2X3_ROTRH Inner capsid protein that self-assembles to form an icosahedral capsid with a T=2 symmetry, which consists of 120 copies of VP2, with channels at each of its five-fold vertices. This capsid constitutes the innermost concentric layer of the viral mature particle. It encapsidates the polymerase VP1, the capping enzyme VP3 and the genomic dsRNA, thereby defining the core. The innermost VP2 capsid and the intermediate VP6 capsid remain intact following cell entry to protect the dsRNA from degradation and to prevent unfavorable antiviral responses in the host cell during all the replication cycle of the virus. Nascent transcripts are transcribed within the structural confines of this double-layered particle (DLP) and are extruded through the channels formed by VP2 N-termini. VP2 is required for the replicase activity of VP1 polymerase. Probably recruits a copy of a VP1-VP3 complex, potentially along with a segment of plus-strand RNA, as a decamer of VP2 assembles. May activate the autoinhibited VP1/RNA complex to coordinate packaging and genome replication.[RuleBase:RU363125]
Publication Abstract from PubMed
Non-enveloped viruses of different types have evolved distinct mechanisms for penetrating a cellular membrane during infection. Rotavirus penetration appears to occur by a process resembling enveloped-virus fusion: membrane distortion linked to conformational changes in a viral protein. Evidence for such a mechanism comes from crystallographic analyses of fragments of VP4, the rotavirus-penetration protein, and infectivity analyses of structure-based VP4 mutants. We describe here the structure of an infectious rotavirus particle determined by electron cryomicroscopy (cryoEM) and single-particle analysis at about 4.3 A resolution. The cryoEM image reconstruction permits a nearly complete trace of the VP4 polypeptide chain, including the positions of most side chains. It shows how the two subfragments of VP4 (VP8(*) and VP5(*)) retain their association after proteolytic cleavage, reveals multiple structural roles for the beta-barrel domain of VP5(*), and specifies interactions of VP4 with other capsid proteins. The virion model allows us to integrate structural and functional information into a coherent mechanism for rotavirus entry.
Atomic model of an infectious rotavirus particle.,Settembre EC, Chen JZ, Dormitzer PR, Grigorieff N, Harrison SC EMBO J. 2011 Jan 19;30(2):408-16. Epub 2010 Dec 14. PMID:21157433[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Settembre EC, Chen JZ, Dormitzer PR, Grigorieff N, Harrison SC. Atomic model of an infectious rotavirus particle. EMBO J. 2011 Jan 19;30(2):408-16. Epub 2010 Dec 14. PMID:21157433 doi:10.1038/emboj.2010.322
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