2r7q: Difference between revisions

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 ==Crystal Structure of VP1 apoenzyme of Rotavirus SA11 (C-terminal hexahistidine-tagged)==
-<StructureSection load='2r7q' size='340' side='right' caption='[[2r7q]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+<StructureSection load='2r7q' size='340' side='right'caption='[[2r7q]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2r7q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Simian_rotavirus Simian rotavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R7Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R7Q FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2r7q]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Simian_rotavirus Simian rotavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R7Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R7Q FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2r7o|2r7o]], [[2r7r|2r7r]], [[2r7s|2r7s]], [[2r7t|2r7t]], [[2r7u|2r7u]], [[2r7v|2r7v]], [[2r7w|2r7w]], [[2r7x|2r7x]]</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]] 2.9&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gene 1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10922 Simian rotavirus])</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=2r7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r7q OCA], [https://pdbe.org/2r7q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r7q RCSB], [https://www.ebi.ac.uk/pdbsum/2r7q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r7q ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2r7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r7q OCA], [http://pdbe.org/2r7q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r7q RCSB], [http://www.ebi.ac.uk/pdbsum/2r7q PDBsum]</span></td></tr>
 </table>
 == 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>
+[https://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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r7/2r7q_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r7/2r7q_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
-</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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2r7q ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Rotavirus RNA-dependent RNA polymerase VP1 catalyzes RNA synthesis within a subviral particle. This activity depends on core shell protein VP2. A conserved sequence at the 3' end of plus-strand RNA templates is important for polymerase association and genome replication. We have determined the structure of VP1 at 2.9 A resolution, as apoenzyme and in complex with RNA. The cage-like enzyme is similar to reovirus lambda3, with four tunnels leading to or from a central, catalytic cavity. A distinguishing characteristic of VP1 is specific recognition, by conserved features of the template-entry channel, of four bases, UGUG, in the conserved 3' sequence. Well-defined interactions with these bases position the RNA so that its 3' end overshoots the initiating register, producing a stable but catalytically inactive complex. We propose that specific 3' end recognition selects rotavirus RNA for packaging and that VP2 activates the autoinhibited VP1/RNA complex to coordinate packaging and genome replication.
-Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1.,Lu X, McDonald SM, Tortorici MA, Tao YJ, Vasquez-Del Carpio R, Nibert ML, Patton JT, Harrison SC Structure. 2008 Nov 12;16(11):1678-88. PMID:19000820<ref>PMID:19000820</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2r7q" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[RNA polymerase|RNA polymerase]]
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Simian rotavirus]]
-[[Category: Harrison, S C]]
+[[Category: Harrison SC]]
-[[Category: Lu, X]]
+[[Category: Lu X]]
-[[Category: Nibert, M L]]
+[[Category: Nibert ML]]
-[[Category: Patton, J T]]
+[[Category: Patton JT]]
-[[Category: Tao, Y J]]
+[[Category: Tao YJ]]
-[[Category: Finger]]
-[[Category: Palm]]
-[[Category: Right hand configuration]]
-[[Category: Rna-dependent rna polymerase]]
-[[Category: Rna-directed rna polymerase]]
-[[Category: Single subunit polymerase fold]]
-[[Category: Thumb]]
-[[Category: Transferase]]
-[[Category: Viral protein]]