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| <SX load='4f5x' size='340' side='right' viewer='molstar' caption='[[4f5x]], [[Resolution|resolution]] 5.00Å' scene=''> | | <SX load='4f5x' size='340' side='right' viewer='molstar' caption='[[4f5x]], [[Resolution|resolution]] 5.00Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[4f5x]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovine_rotavirus Bovine rotavirus], [http://en.wikipedia.org/wiki/Bovine_rotavirus_a Bovine rotavirus a] and [http://en.wikipedia.org/wiki/Simian_11_rotavirus Simian 11 rotavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F5X OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=4F5X FirstGlance]. <br> | | <table><tr><td colspan='2'>[[4f5x]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Bovine_rotavirus_A Bovine rotavirus A], [https://en.wikipedia.org/wiki/Bovine_rotavirus_strain_NCDV/G6 Bovine rotavirus strain NCDV/G6] and [https://en.wikipedia.org/wiki/Simian_11_rotavirus_(serotype_3_/_strain_SA11-Patton) Simian 11 rotavirus (serotype 3 / strain SA11-Patton)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F5X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4F5X FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 5Å</td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kz4|3kz4]], [[2r7s|2r7s]]</td></tr> | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-directed_RNA_polymerase RNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.48 2.7.7.48] </span></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=4f5x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f5x OCA], [https://pdbe.org/4f5x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4f5x RCSB], [https://www.ebi.ac.uk/pdbsum/4f5x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4f5x 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=4f5x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f5x OCA], [http://pdbe.org/4f5x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4f5x RCSB], [http://www.ebi.ac.uk/pdbsum/4f5x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4f5x ProSAT]</span></td></tr> | |
| </table> | | </table> |
| == Function == | | == Function == |
| [[http://www.uniprot.org/uniprot/RDRP_ROTSP RDRP_ROTSP]] RNA-directed RNA polymerase that is involved in both transcription and genome replication. Together with VP3 capping enzyme, forms an enzyme complex positioned near the channels situated at each of the five-fold vertices of the core. Following infection, the outermost layer of the virus is lost, leaving a double-layered particle (DLP) made up of the core and VP6 shell. VP1 then catalyzes the transcription of fully conservative plus-strand genomic RNAs that are extruded through the DLP's channels into the cytoplasm where they function as mRNAs for translation of viral proteins. One copy of each of the viral (+)RNAs is also recruited during core assembly, together with newly synthesized polymerase complexes and VP2. The polymerase of these novo-formed particles catalyzes the synthesis of complementary minus-strands leading to dsRNA formation. To do so, the polymerase specifically recognizes and binds 4 bases 5'-UGUG-3' in the conserved 3'-sequence of plus-strand RNA templates. VP2 presumably activates the autoinhibited VP1-RNA complex to coordinate packaging and genome replication. Once dsRNA synthesis is complete, the polymerase switches to the transcriptional mode, thus providing secondary transcription.<ref>PMID:9371626</ref> <ref>PMID:19000820</ref> [[http://www.uniprot.org/uniprot/VP6_ROTBN VP6_ROTBN]] 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/H9N1A6_9REOV H9N1A6_9REOV] |
| <div style="background-color:#fffaf0;">
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| == Publication Abstract from PubMed ==
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| Double-stranded RNA (dsRNA) viruses transcribe and replicate RNA within an assembled, inner capsid particle; only plus-sense mRNA emerges into the intracellular milieu. During infectious entry of a rotavirus particle, the outer layer of its three-layer structure dissociates, delivering the inner double-layered particle (DLP) into the cytosol. DLP structures determined by X-ray crystallography and electron cryomicroscopy (cryoEM) show that the RNA coils uniformly into the particle interior, avoiding a "fivefold hub" of more structured density projecting inward from the VP2 shell of the DLP along each of the twelve 5-fold axes. Analysis of the X-ray crystallographic electron density map suggested that principal contributors to the hub are the N-terminal arms of VP2, but reexamination of the cryoEM map has shown that many features come from a molecule of VP1, randomly occupying five equivalent and partly overlapping positions. We confirm here that the electron density in the X-ray map leads to the same conclusion, and we describe the functional implications of the orientation and position of the polymerase. The exit channel for the nascent transcript directs the nascent transcript toward an opening along the 5-fold axis. The template strand enters from within the particle, and the dsRNA product of the initial replication step exits in a direction tangential to the inner surface of the VP2 shell, allowing it to coil optimally within the DLP. The polymerases of reoviruses appear to have similar positions and functional orientations.
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| Location of the dsRNA-Dependent Polymerase, VP1, in Rotavirus Particles.,Estrozi LF, Settembre EC, Goret G, McClain B, Zhang X, Chen JZ, Grigorieff N, Harrison SC J Mol Biol. 2012 Oct 23. pii: S0022-2836(12)00829-7. doi:, 10.1016/j.jmb.2012.10.011. PMID:23089332<ref>PMID:23089332</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 4f5x" style="background-color:#fffaf0;"></div>
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| ==See Also== | | ==See Also== |
| *[[RNA polymerase 3D structures|RNA polymerase 3D structures]] | | *[[RNA polymerase 3D structures|RNA polymerase 3D structures]] |
| == References ==
| | *[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]] |
| <references/>
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| __TOC__ | | __TOC__ |
| </SX> | | </SX> |
| [[Category: Bovine rotavirus]] | | [[Category: Bovine rotavirus A]] |
| [[Category: Bovine rotavirus a]] | | [[Category: Bovine rotavirus strain NCDV/G6]] |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
| [[Category: RNA-directed RNA polymerase]]
| | [[Category: Chen JZ]] |
| [[Category: Simian 11 rotavirus]]
| | [[Category: Estrozi LF]] |
| [[Category: Chen, J Z]] | | [[Category: Goret G]] |
| [[Category: Estrozi, L F]] | | [[Category: Grigorieff N]] |
| [[Category: Goret, G]] | | [[Category: Harrison SC]] |
| [[Category: Grigorieff, N]] | | [[Category: McClain B]] |
| [[Category: Harrison, S C]] | | [[Category: Settembre EC]] |
| [[Category: McClain, B]] | | [[Category: Zhang X]] |
| [[Category: Settembre, E C]] | |
| [[Category: Zhang, X]] | |
| [[Category: Beta-jellyroll]]
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| [[Category: Polymerase]]
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| [[Category: Transcriptase]]
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| [[Category: Virus]]
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