1qhd - Revision history

OCA at 23:48, 27 December 2023

2023-12-27T23:48:34Z

←Older revision		Revision as of 23:48, 27 December 2023
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	<StructureSection load='1qhd' size='340' side='right'caption='[[1qhd]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='1qhd' size='340' side='right'caption='[[1qhd]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qhd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QHD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qhd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bovine_rotavirus_strain_RF Bovine rotavirus strain RF]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QHD FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>~~, ~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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]] 1.95Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1qhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qhd OCA], [https://pdbe.org/1qhd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qhd RCSB], [https://www.ebi.ac.uk/pdbsum/1qhd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qhd 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=1qhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qhd OCA], [https://pdbe.org/1qhd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qhd RCSB], [https://www.ebi.ac.uk/pdbsum/1qhd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qhd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/VP6_ROTRF VP6_ROTRF]] 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.<ref>PMID:6292454</ref>	+	[https://www.uniprot.org/uniprot/VP6_ROTRF VP6_ROTRF] 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.<ref>PMID:6292454</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bovine rotavirus strain RF]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Mathieu, M]]	+	[[Category: Mathieu M]]
-	[[Category: Petitpas, I]]	+	[[Category: Petitpas I]]
-	[[Category: Rey~~, F A]]~~	+	[[Category: Rey FA]]
-	~~[[Category: Viral capsid protein]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 09:57, 15 September 2021

2021-09-15T09:57:05Z

←Older revision		Revision as of 09:57, 15 September 2021
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	<StructureSection load='1qhd' size='340' side='right'caption='[[1qhd]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='1qhd' size='340' side='right'caption='[[1qhd]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qhd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QHD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1QHD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qhd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QHD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></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=1qhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qhd OCA], [~~http~~://pdbe.org/1qhd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1qhd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1qhd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1qhd 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=1qhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qhd OCA], [https://pdbe.org/1qhd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qhd RCSB], [https://www.ebi.ac.uk/pdbsum/1qhd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qhd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/VP6_ROTRF VP6_ROTRF]] 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.<ref>PMID:6292454</ref>	+	[[https://www.uniprot.org/uniprot/VP6_ROTRF VP6_ROTRF]] 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.<ref>PMID:6292454</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Virus coat ~~protein~~\|Virus coat ~~protein~~]]	+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:02, 27 November 2019

2019-11-27T10:02:58Z

←Older revision		Revision as of 10:02, 27 November 2019
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF VP6, THE MAJOR CAPSID PROTEIN OF GROUP A ROTAVIRUS==		==CRYSTAL STRUCTURE OF VP6, THE MAJOR CAPSID PROTEIN OF GROUP A ROTAVIRUS==
-	<StructureSection load='1qhd' size='340' side='right' caption='[[1qhd]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='1qhd' size='340' side='right'caption='[[1qhd]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qhd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QHD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qhd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QHD FirstGlance]. <br>
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1qhd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1qhd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Virus coat protein\|Virus coat protein]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Mathieu, M]]		[[Category: Mathieu, M]]
	[[Category: Petitpas, I]]		[[Category: Petitpas, I]]

OCA at 08:04, 24 February 2018

2018-02-24T08:04:10Z

←Older revision		Revision as of 08:04, 24 February 2018
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF VP6, THE MAJOR CAPSID PROTEIN OF GROUP A ROTAVIRUS==		==CRYSTAL STRUCTURE OF VP6, THE MAJOR CAPSID PROTEIN OF GROUP A ROTAVIRUS==
	<StructureSection load='1qhd' size='340' side='right' caption='[[1qhd]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='1qhd' size='340' side='right' caption='[[1qhd]], [[Resolution\|resolution]] 1.95Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></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=1qhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qhd OCA], [http://pdbe.org/1qhd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qhd RCSB], [http://www.ebi.ac.uk/pdbsum/1qhd 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=1qhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qhd OCA], [http://pdbe.org/1qhd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qhd RCSB], [http://www.ebi.ac.uk/pdbsum/1qhd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1qhd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qh/1qhd_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qh/1qhd_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>
	</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=1qhd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 1qhd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1qhd" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Virus coat protein\|Virus coat protein]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 00:36, 12 September 2015

2015-09-12T00:36:38Z

←Older revision		Revision as of 00:36, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='1qhd' size='340' side='right' caption='[[1qhd]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='1qhd' size='340' side='right' caption='[[1qhd]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qhd]] is a 1 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Bovine_rotavirus Bovine rotavirus]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QHD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qhd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QHD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SEGMENT 6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10927 Bovine 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=1qhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qhd OCA], [http://pdbe.org/1qhd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qhd RCSB], [http://www.ebi.ac.uk/pdbsum/1qhd 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=1qhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qhd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qhd RCSB], [http://www.ebi.ac.uk/pdbsum/1qhd PDBsum]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~VS06_ROTBR VS06_ROTBR~~]] 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.<ref>PMID:6292454</ref>	+	[[http://www.uniprot.org/uniprot/VP6_ROTRF VP6_ROTRF]] 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.<ref>PMID:6292454</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		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 1qhd" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bovine rotavirus]]
	[[Category: Mathieu, M]]		[[Category: Mathieu, M]]
	[[Category: Petitpas, I]]		[[Category: Petitpas, I]]

OCA at 21:30, 25 December 2014

2014-12-25T21:30:37Z

←Older revision		Revision as of 21:30, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qhd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovine_rotavirus Bovine rotavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QHD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qhd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovine_rotavirus Bovine rotavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QHD FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SEGMENT 6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10927 Bovine rotavirus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SEGMENT 6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10927 Bovine 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=1qhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qhd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qhd RCSB], [http://www.ebi.ac.uk/pdbsum/1qhd 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=1qhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qhd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qhd RCSB], [http://www.ebi.ac.uk/pdbsum/1qhd PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VS06_ROTBR VS06_ROTBR]] 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.<ref>PMID:6292454</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Bovine rotavirus]]		[[Category: Bovine rotavirus]]
-	[[Category: Mathieu, M.]]	+	[[Category: Mathieu, M]]
-	[[Category: Petitpas, I.]]	+	[[Category: Petitpas, I]]
-	[[Category: Rey, F A.]]	+	[[Category: Rey, F A]]
	[[Category: Viral capsid protein]]		[[Category: Viral capsid protein]]
	[[Category: Viral protein]]		[[Category: Viral protein]]

OCA at 22:48, 28 September 2014

2014-09-28T22:48:23Z

←Older revision		Revision as of 22:48, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1qhd.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF VP6, THE MAJOR CAPSID PROTEIN OF GROUP A ROTAVIRUS==
		+	<StructureSection load='1qhd' size='340' side='right' caption='[[1qhd]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1qhd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovine_rotavirus Bovine rotavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QHD FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SEGMENT 6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10927 Bovine 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=1qhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qhd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qhd RCSB], [http://www.ebi.ac.uk/pdbsum/1qhd 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/qh/1qhd_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 ==
		+	The structural protein VP6 of rotavirus, an important pathogen responsible for severe gastroenteritis in children, forms the middle layer in the triple-layered viral capsid. Here we present the crystal structure of VP6 determined to 2 A resolution and describe its interactions with other capsid proteins by fitting the atomic model into electron cryomicroscopic reconstructions of viral particles. VP6, which forms a tight trimer, has two distinct domains: a distal beta-barrel domain and a proximal alpha-helical domain, which interact with the outer and inner layer of the virion, respectively. The overall fold is similar to that of protein VP7 from bluetongue virus, with the subunits wrapping about a central 3-fold axis. A distinguishing feature of the VP6 trimer is a central Zn(2+) ion located on the 3-fold molecular axis. The crude atomic model of the middle layer derived from the fit shows that quasi-equivalence is only partially obeyed by VP6 in the T = 13 middle layer and suggests a model for the assembly of the 260 VP6 trimers onto the T = 1 viral inner layer.

-	~~{{STRUCTURE_1qhd\| PDB=1qhd \| SCENE= }}~~	+	Atomic structure of the major capsid protein of rotavirus: implications for the architecture of the virion.,Mathieu M, Petitpas I, Navaza J, Lepault J, Kohli E, Pothier P, Prasad BV, Cohen J, Rey FA EMBO J. 2001 Apr 2;20(7):1485-97. PMID:11285213<ref>PMID:11285213</ref>

-	~~===CRYSTAL STRUCTURE OF VP6~~, ~~THE MAJOR CAPSID PROTEIN OF GROUP A ROTAVIRUS===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11285213}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1qhd]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bovine_rotavirus Bovine rotavirus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1QHD OCA].~~	+

	==See Also==		==See Also==
	*[[Virus coat protein\|Virus coat protein]]		*[[Virus coat protein\|Virus coat protein]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:011285213<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Bovine rotavirus]]		[[Category: Bovine rotavirus]]
	[[Category: Mathieu, M.]]		[[Category: Mathieu, M.]]

OCA: Protected "1qhd" [edit=sysop:move=sysop]

2012-10-20T21:53:45Z

Protected "1qhd" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:53, 20 October 2012

OCA at 21:53, 20 October 2012

2012-10-20T21:53:43Z

←Older revision		Revision as of 21:53, 20 October 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1qhd.png\|left\|200px]]		[[Image:1qhd.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1qhd", 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_1qhd\| PDB=1qhd \| SCENE= }}		{{STRUCTURE_1qhd\| PDB=1qhd \| SCENE= }}

	===CRYSTAL STRUCTURE OF VP6, THE MAJOR CAPSID PROTEIN OF GROUP A ROTAVIRUS===		===CRYSTAL STRUCTURE OF VP6, THE MAJOR CAPSID PROTEIN OF GROUP A ROTAVIRUS===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11285213}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11285213 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_11285213}}		{{ABSTRACT_PUBMED_11285213}}

	==About this Structure==		==About this Structure==
-	~~1QHD~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Bovine_rotavirus Bovine rotavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QHD OCA].	+	[[1qhd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovine_rotavirus Bovine rotavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QHD OCA].
		+
		+	==See Also==
		+	*[[Virus coat protein\|Virus coat protein]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~11285213~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011285213</ref><references group="xtra"/>
	[[Category: Bovine rotavirus]]		[[Category: Bovine rotavirus]]
	[[Category: Mathieu, M.]]		[[Category: Mathieu, M.]]
Line 29:		Line 20:
	[[Category: Rey, F A.]]		[[Category: Rey, F A.]]
	[[Category: Viral capsid protein]]		[[Category: Viral capsid protein]]
-		+	[[Category: Viral protein]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Wed Feb 18 08:19:42 2009''~~	+

OCA at 06:19, 18 February 2009

2009-02-18T06:19:44Z

←Older revision		Revision as of 06:19, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1QHD is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Bovine_rotavirus Bovine rotavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QHD OCA].	+	1QHD is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Bovine_rotavirus Bovine rotavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QHD OCA].

	==Reference==		==Reference==
-	Atomic structure of the major capsid protein of rotavirus: implications for the architecture of the virion., Mathieu M, Petitpas I, Navaza J, Lepault J, Kohli E, Pothier P, Prasad BV, Cohen J, Rey FA, EMBO J. 2001 Apr 2;20(7):1485-97. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/11285213 11285213]~~	+	<ref group="xtra">PMID:11285213</ref><references group="xtra"/>
	[[Category: Bovine rotavirus]]		[[Category: Bovine rotavirus]]
-	[[Category: Single protein]]
	[[Category: Mathieu, M.]]		[[Category: Mathieu, M.]]
	[[Category: Petitpas, I.]]		[[Category: Petitpas, I.]]
Line 31:		Line 30:
	[[Category: Viral capsid protein]]		[[Category: Viral capsid protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 14~~:39:~~30 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 08:19:42 2009''