2r7t - Revision history

OCA at 09:20, 21 February 2024

OCA — Wed, 21 Feb 2024 09:20:34 GMT

←Older revision		Revision as of 09:20, 21 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2r7t]] is a 2 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=2R7T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R7T FirstGlance]. <br>		<table><tr><td colspan='2'>[[2r7t]] is a 2 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=2R7T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R7T FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[2r7o\|2r7o]], [[2r7q\|2r7q]], [[2r7r\|2r7r]], [[2r7s\|2r7s]], [[2r7u\|2r7u]], [[2r7v\|2r7v]], [[2r7w\|2r7w]], [[2r7x\|2r7x]]</div></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]] 3Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">gene 1 ([https://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=2r7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r7t OCA], [https://pdbe.org/2r7t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r7t RCSB], [https://www.ebi.ac.uk/pdbsum/2r7t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r7t ProSAT]</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=2r7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r7t OCA], [https://pdbe.org/2r7t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r7t RCSB], [https://www.ebi.ac.uk/pdbsum/2r7t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r7t ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[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>	+	[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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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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=2r7t 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=2r7t ConSurf].
	<div style="clear:both"></div>		<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®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2r7t" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 38:		Line 28:
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Simian rotavirus]]		[[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-rna complex]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 04:17, 2 July 2021

OCA — Fri, 02 Jul 2021 04:17:22 GMT

←Older revision		Revision as of 04:17, 2 July 2021
Line 1:		Line 1:

	==Crystal Structure of Rotavirus SA11 VP1/RNA (UGUGAACC) Complex==		==Crystal Structure of Rotavirus SA11 VP1/RNA (UGUGAACC) Complex==
-	<StructureSection load='2r7t' size='340' side='right' caption='[[2r7t]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='2r7t' size='340' side='right'caption='[[2r7t]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2r7t]] is a 2 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=2R7T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2R7T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2r7t]] is a 2 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=2R7T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R7T FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r7o\|2r7o]], [[2r7q\|2r7q]], [[2r7r\|2r7r]], [[2r7s\|2r7s]], [[2r7u\|2r7u]], [[2r7v\|2r7v]], [[2r7w\|2r7w]], [[2r7x\|2r7x]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2r7o\|2r7o]], [[2r7q\|2r7q]], [[2r7r\|2r7r]], [[2r7s\|2r7s]], [[2r7u\|2r7u]], [[2r7v\|2r7v]], [[2r7w\|2r7w]], [[2r7x\|2r7x]]</div></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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gene 1 ([https://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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2r7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r7t OCA], [~~http~~://pdbe.org/2r7t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2r7t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2r7t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2r7t ProSAT]</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=2r7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r7t OCA], [https://pdbe.org/2r7t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r7t RCSB], [https://www.ebi.ac.uk/pdbsum/2r7t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r7t 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>	+	[[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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r7/2r7t_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r7/2r7t_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2r7t" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2r7t" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Simian rotavirus]]		[[Category: Simian rotavirus]]
	[[Category: Harrison, S C]]		[[Category: Harrison, S C]]

OCA at 07:44, 25 October 2017

OCA — Wed, 25 Oct 2017 07:44:53 GMT

←Older revision		Revision as of 07:44, 25 October 2017
Line 1:		Line 1:
		+
	==Crystal Structure of Rotavirus SA11 VP1/RNA (UGUGAACC) Complex==		==Crystal Structure of Rotavirus SA11 VP1/RNA (UGUGAACC) Complex==
	<StructureSection load='2r7t' size='340' side='right' caption='[[2r7t]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2r7t' size='340' side='right' caption='[[2r7t]], [[Resolution\|resolution]] 3.00Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r7o\|2r7o]], [[2r7q\|2r7q]], [[2r7r\|2r7r]], [[2r7s\|2r7s]], [[2r7u\|2r7u]], [[2r7v\|2r7v]], [[2r7w\|2r7w]], [[2r7x\|2r7x]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r7o\|2r7o]], [[2r7q\|2r7q]], [[2r7r\|2r7r]], [[2r7s\|2r7s]], [[2r7u\|2r7u]], [[2r7v\|2r7v]], [[2r7w\|2r7w]], [[2r7x\|2r7x]]</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='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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2r7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r7t OCA], [http://pdbe.org/2r7t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r7t RCSB], [http://www.ebi.ac.uk/pdbsum/2r7t PDBsum]</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=2r7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r7t OCA], [http://pdbe.org/2r7t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r7t RCSB], [http://www.ebi.ac.uk/pdbsum/2r7t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2r7t ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2r7t" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2r7t" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[RNA polymerase\|RNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:24, 8 February 2016

OCA — Mon, 08 Feb 2016 16:24:34 GMT

←Older revision		Revision as of 16:24, 8 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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=2r7t ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:22, 10 September 2015

OCA — Thu, 10 Sep 2015 13:22:03 GMT

←Older revision		Revision as of 13:22, 10 September 2015
Line 5:		Line 5:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r7o\|2r7o]], [[2r7q\|2r7q]], [[2r7r\|2r7r]], [[2r7s\|2r7s]], [[2r7u\|2r7u]], [[2r7v\|2r7v]], [[2r7w\|2r7w]], [[2r7x\|2r7x]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r7o\|2r7o]], [[2r7q\|2r7q]], [[2r7r\|2r7r]], [[2r7s\|2r7s]], [[2r7u\|2r7u]], [[2r7v\|2r7v]], [[2r7w\|2r7w]], [[2r7x\|2r7x]]</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='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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2r7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r7t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r7t RCSB], [http://www.ebi.ac.uk/pdbsum/2r7t PDBsum]</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=2r7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r7t OCA], [http://pdbe.org/2r7t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r7t RCSB], [http://www.ebi.ac.uk/pdbsum/2r7t PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2r7t" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 00:37, 25 December 2014

OCA — Thu, 25 Dec 2014 00:37:39 GMT

←Older revision		Revision as of 00:37, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2r7t]] is a 2 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=2R7T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R7T FirstGlance]. <br>		<table><tr><td colspan='2'>[[2r7t]] is a 2 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=2R7T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R7T FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r7o\|2r7o]], [[2r7q\|2r7q]], [[2r7r\|2r7r]], [[2r7s\|2r7s]], [[2r7u\|2r7u]], [[2r7v\|2r7v]], [[2r7w\|2r7w]], [[2r7x\|2r7x]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r7o\|2r7o]], [[2r7q\|2r7q]], [[2r7r\|2r7r]], [[2r7s\|2r7s]], [[2r7u\|2r7u]], [[2r7v\|2r7v]], [[2r7w\|2r7w]], [[2r7x\|2r7x]]</td></tr>
-	<tr><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='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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2r7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r7t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r7t RCSB], [http://www.ebi.ac.uk/pdbsum/2r7t PDBsum]</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=2r7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r7t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r7t RCSB], [http://www.ebi.ac.uk/pdbsum/2r7t PDBsum]</span></td></tr>
-	<table>	+	</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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Simian rotavirus]]		[[Category: Simian rotavirus]]
-	[[Category: Harrison, S C.]]	+	[[Category: Harrison, S C]]
-	[[Category: Lu, X.]]	+	[[Category: Lu, X]]
-	[[Category: Nibert, M L.]]	+	[[Category: Nibert, M L]]
-	[[Category: Patton, J T.]]	+	[[Category: Patton, J T]]
-	[[Category: Tao, Y J.]]	+	[[Category: Tao, Y J]]
	[[Category: Finger]]		[[Category: Finger]]
	[[Category: Palm]]		[[Category: Palm]]

OCA at 06:31, 29 September 2014

OCA — Mon, 29 Sep 2014 06:31:36 GMT

←Older revision		Revision as of 06:31, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2r7t.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Rotavirus SA11 VP1/RNA (UGUGAACC) Complex==
		+	<StructureSection load='2r7t' size='340' side='right' caption='[[2r7t]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2r7t]] is a 2 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=2R7T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R7T FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r7o\|2r7o]], [[2r7q\|2r7q]], [[2r7r\|2r7r]], [[2r7s\|2r7s]], [[2r7u\|2r7u]], [[2r7v\|2r7v]], [[2r7w\|2r7w]], [[2r7x\|2r7x]]</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2r7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r7t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r7t RCSB], [http://www.ebi.ac.uk/pdbsum/2r7t PDBsum]</span></td></tr>
		+	<table>
		+	== 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/r7/2r7t_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].
		+	<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.

-	~~{{STRUCTURE_2r7t\| PDB=2r7t \| SCENE= }}~~	+	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>

-	~~===Crystal Structure of Rotavirus SA11 VP1~~/~~RNA (UGUGAACC) Complex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19000820}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2r7t]] is~~ a ~~2 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=2R7T OCA].~~	+

	==See Also==		==See Also==
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase\|RNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019000820<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Simian rotavirus]]		[[Category: Simian rotavirus]]
	[[Category: Harrison, S C.]]		[[Category: Harrison, S C.]]

OCA at 10:44, 20 October 2012

OCA — Sat, 20 Oct 2012 10:44:42 GMT

←Older revision		Revision as of 10:44, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2r7t]] is a 2 chain structure ~~of [[RNA polymerase]]~~ 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=2R7T OCA].	+	[[2r7t]] is a 2 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=2R7T OCA].

	==See Also==		==See Also==

OCA: Protected "2r7t" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 03:07:55 GMT

Protected "2r7t" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:07, 26 July 2012

OCA at 03:07, 26 July 2012

OCA — Thu, 26 Jul 2012 03:07:53 GMT

←Older revision		Revision as of 03:07, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2r7t.png\|left\|200px]]		[[Image:2r7t.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2r7t", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2r7t\| PDB=2r7t \| SCENE= }}		{{STRUCTURE_2r7t\| PDB=2r7t \| SCENE= }}

	===Crystal Structure of Rotavirus SA11 VP1/RNA (UGUGAACC) Complex===		===Crystal Structure of Rotavirus SA11 VP1/RNA (UGUGAACC) Complex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19000820}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19000820 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19000820}}		{{ABSTRACT_PUBMED_19000820}}

	==About this Structure==		==About this Structure==
-	~~2R7T~~ is a 2 ~~chains~~ structure with ~~sequences~~ 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=2R7T OCA].	+	[[2r7t]] is a 2 chain structure of [[RNA polymerase]] 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=2R7T OCA].
		+
		+	==See Also==
		+	*[[RNA polymerase\|RNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19000820~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019000820</ref><references group="xtra"/>
	[[Category: Simian rotavirus]]		[[Category: Simian rotavirus]]
	[[Category: Harrison, S C.]]		[[Category: Harrison, S C.]]
Line 39:		Line 30:
	[[Category: Transferase-rna complex]]		[[Category: Transferase-rna complex]]
	[[Category: Viral protein]]		[[Category: Viral protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 14 08:59:30 2010''