3gzu - Revision history

OCA at 09:57, 21 February 2024

2024-02-21T09:57:28Z

←Older revision		Revision as of 09:57, 21 February 2024
Line 3:		Line 3:
	<SX load='3gzu' size='340' side='right' viewer='molstar' caption='[[3gzu]], [[Resolution\|resolution]] 3.80Å' scene=''>		<SX load='3gzu' size='340' side='right' viewer='molstar' caption='[[3gzu]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gzu]] is a 15 chain structure with sequence from [https://en.wikipedia.org/wiki/ ] and [https://en.wikipedia.org/wiki/~~Group_a_rotaviruses Group a rotaviruses~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GZU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gzu]] is a 15 chain structure with sequence from [https://en.wikipedia.org/wiki/Rotavirus_A Rotavirus A] and [https://en.wikipedia.org/wiki/Simian_rotavirus_A_strain_RRV Simian rotavirus A strain RRV]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GZU 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">Electron Microscopy, [[Resolution\|Resolution]] 3.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3gzt\|3gzt]]~~</~~div~~></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gzu OCA], [https://pdbe.org/3gzu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gzu RCSB], [https://www.ebi.ac.uk/pdbsum/3gzu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gzu 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=3gzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gzu OCA], [https://pdbe.org/3gzu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gzu RCSB], [https://www.ebi.ac.uk/pdbsum/3gzu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gzu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~VP2_ROTW3 VP2_ROTW3~~]] 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. 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. VP2 is required for the replicase activity of VP1 polymerase. It probably plays a role in the coordination of packaging and genome replication by controlling the initiation of minus-strand synthesis. Binding to the polymerase VP1 presumably activates the autoinhibited VP1-RNA complex which will start the synthesis of the complementary minus-strand (By similarity). [[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/B2BMD1_9VIRU B2BMD1_9VIRU]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</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=3gzu 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=3gzu ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Rotaviruses, major causes of childhood gastroenteritis, are nonenveloped, icosahedral particles with double-strand RNA genomes. By the use of electron cryomicroscopy and single-particle reconstruction, we have visualized a rotavirus particle comprising the inner capsid coated with the trimeric outer-layer protein, VP7, at a resolution (4 A) comparable with that of X-ray crystallography. We have traced the VP7 polypeptide chain, including parts not seen in its X-ray crystal structure. The 3 well-ordered, 30-residue, N-terminal "arms" of each VP7 trimer grip the underlying trimer of VP6, an inner-capsid protein. Structural differences between free and particle-bound VP7 and between free and VP7-coated inner capsids may regulate mRNA transcription and release. The Ca(2+)-stabilized VP7 intratrimer contact region, which presents important neutralizing epitopes, is unaltered upon capsid binding.
-
-	Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM.,Chen JZ, Settembre EC, Aoki ST, Zhang X, Bellamy AR, Dormitzer PR, Harrison SC, Grigorieff N Proc Natl Acad Sci U S A. 2009 Jun 30;106(26):10644-8. Epub 2009 Jun 1. PMID:19487668<ref>PMID:19487668</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3gzu" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]		*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: Group a rotaviruses]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Chen, J Z]]~~	+	[[Category: Rotavirus A]]
-	~~[[Category: Grigorieff, N]]~~	+	[[Category: Simian rotavirus A strain RRV]]
-	~~[[Category: Harrison, S C]]~~	+	[[Category: Chen JZ]]
-	~~[[Category: Settembre, E C]]~~	+	[[Category: Grigorieff N]]
-	~~[[Category: Capsid protein]]~~	+	[[Category: Harrison SC]]
-	~~[[Category: Core protein]]~~	+	[[Category: Settembre EC]]
-	~~[[Category: Dlp]]~~	+
-	~~[[Category: Icosaderal virus]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Rna-binding]]~~	+
-	[[Category: Rotavirus]]	+
-	[[Category: ~~Virion~~]]	+
-	[[Category: ~~Virus~~]]	+
-	[[Category: ~~Vp2~~]]	+
-	[[Category: ~~Vp6~~]]	+
-	[[Category: ~~Vp7]]~~	+
-	~~[[Category: Zinc~~]]	+

OCA at 07:59, 16 March 2022

2022-03-16T07:59:15Z

←Older revision		Revision as of 07:59, 16 March 2022
Line 3:		Line 3:
	<SX load='3gzu' size='340' side='right' viewer='molstar' caption='[[3gzu]], [[Resolution\|resolution]] 3.80Å' scene=''>		<SX load='3gzu' size='340' side='right' viewer='molstar' caption='[[3gzu]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gzu]] is a 15 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/ ] and [~~http~~://en.wikipedia.org/wiki/Group_a_rotaviruses Group a rotaviruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GZU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3GZU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gzu]] is a 15 chain structure with sequence from [https://en.wikipedia.org/wiki/ ] and [https://en.wikipedia.org/wiki/Group_a_rotaviruses Group a rotaviruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GZU 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='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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gzt\|3gzt]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gzt\|3gzt]]</div></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=3gzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gzu OCA], [~~http~~://pdbe.org/3gzu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3gzu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3gzu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3gzu 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=3gzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gzu OCA], [https://pdbe.org/3gzu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gzu RCSB], [https://www.ebi.ac.uk/pdbsum/3gzu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gzu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/VP2_ROTW3 VP2_ROTW3]] 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. 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. VP2 is required for the replicase activity of VP1 polymerase. It probably plays a role in the coordination of packaging and genome replication by controlling the initiation of minus-strand synthesis. Binding to the polymerase VP1 presumably activates the autoinhibited VP1-RNA complex which will start the synthesis of the complementary minus-strand (By similarity). [[~~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/VP2_ROTW3 VP2_ROTW3]] 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. 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. VP2 is required for the replicase activity of VP1 polymerase. It probably plays a role in the coordination of packaging and genome replication by controlling the initiation of minus-strand synthesis. Binding to the polymerase VP1 presumably activates the autoinhibited VP1-RNA complex which will start the synthesis of the complementary minus-strand (By similarity). [[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]]

OCA at 17:22, 10 April 2020

2020-04-10T17:22:08Z

←Older revision		Revision as of 17:22, 10 April 2020
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	<SX load='3gzu' size='340' side='right' viewer='molstar' caption='[[3gzu]], [[Resolution\|resolution]] 3.80Å' scene=''>		<SX load='3gzu' size='340' side='right' viewer='molstar' caption='[[3gzu]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gzu]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Group_a_rotaviruses Group a rotaviruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GZU OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3GZU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gzu]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Group_a_rotaviruses Group a rotaviruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GZU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3GZU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gzt\|3gzt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gzt\|3gzt]]</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=3gzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gzu OCA], [http://pdbe.org/3gzu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gzu RCSB], [http://www.ebi.ac.uk/pdbsum/3gzu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gzu 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=3gzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gzu OCA], [http://pdbe.org/3gzu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gzu RCSB], [http://www.ebi.ac.uk/pdbsum/3gzu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gzu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 04:24, 5 March 2020

2020-03-05T04:24:58Z

←Older revision		Revision as of 04:24, 5 March 2020
Line 1:		Line 1:

	==VP7 recoated rotavirus DLP==		==VP7 recoated rotavirus DLP==
-	<~~StructureSection~~ load='3gzu' size='340' side='right'caption='[[3gzu]], [[Resolution\|resolution]] 3.80Å' scene=''>	+	<SX load='3gzu' size='340' side='right' viewer='molstar' caption='[[3gzu]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3gzu]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Group_a_rotaviruses Group a rotaviruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GZU FirstGlance]. <br>		<table><tr><td colspan='2'>[[3gzu]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Group_a_rotaviruses Group a rotaviruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GZU FirstGlance]. <br>
Line 35:		Line 35:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Group a rotaviruses]]		[[Category: Group a rotaviruses]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 07:09, 6 November 2019

2019-11-06T07:09:57Z

←Older revision		Revision as of 07:09, 6 November 2019
Line 1:		Line 1:

	==VP7 recoated rotavirus DLP==		==VP7 recoated rotavirus DLP==
-	<StructureSection load='3gzu' size='340' side='right' caption='[[3gzu]], [[Resolution\|resolution]] 3.80Å' scene=''>	+	<StructureSection load='3gzu' size='340' side='right'caption='[[3gzu]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3gzu]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Group_a_rotaviruses Group a rotaviruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GZU FirstGlance]. <br>		<table><tr><td colspan='2'>[[3gzu]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Group_a_rotaviruses Group a rotaviruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GZU FirstGlance]. <br>
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Group a rotaviruses]]		[[Category: Group a rotaviruses]]
		+	[[Category: Large Structures]]
	[[Category: Chen, J Z]]		[[Category: Chen, J Z]]
	[[Category: Grigorieff, N]]		[[Category: Grigorieff, N]]

OCA at 06:03, 7 December 2018

2018-12-07T06:03:48Z

←Older revision		Revision as of 06:03, 7 December 2018
Line 1:		Line 1:
		+
	==VP7 recoated rotavirus DLP==		==VP7 recoated rotavirus DLP==
	<StructureSection load='3gzu' size='340' side='right' caption='[[3gzu]], [[Resolution\|resolution]] 3.80Å' scene=''>		<StructureSection load='3gzu' size='340' side='right' caption='[[3gzu]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gzu]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Group_a_rotaviruses Group a rotaviruses~~] and [http://en.wikipedia.org/wiki/~~Rotrh Rotrh~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GZU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gzu]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Group_a_rotaviruses Group a rotaviruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GZU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gzt\|3gzt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gzt\|3gzt]]</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=3gzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gzu OCA], [http://pdbe.org/3gzu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gzu RCSB], [http://www.ebi.ac.uk/pdbsum/3gzu 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=3gzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gzu OCA], [http://pdbe.org/3gzu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gzu RCSB], [http://www.ebi.ac.uk/pdbsum/3gzu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gzu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gz/3gzu_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gz/3gzu_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 36:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Group a rotaviruses]]		[[Category: Group a rotaviruses]]
-	[[Category: Rotrh]]
	[[Category: Chen, J Z]]		[[Category: Chen, J Z]]
	[[Category: Grigorieff, N]]		[[Category: Grigorieff, N]]
Line 53:		Line 53:
	[[Category: Vp6]]		[[Category: Vp6]]
	[[Category: Vp7]]		[[Category: Vp7]]
		+	[[Category: Zinc]]

OCA at 11:59, 7 February 2016

2016-02-07T11:59:25Z

←Older revision		Revision as of 11:59, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='3gzu' size='340' side='right' caption='[[3gzu]], [[Resolution\|resolution]] 3.80Å' scene=''>		<StructureSection load='3gzu' size='340' side='right' caption='[[3gzu]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gzu]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rhesus_rotavirus Rhesus rotavirus~~] and [http://en.wikipedia.org/wiki/~~Rotavirus_a Rotavirus a~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GZU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gzu]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/Group_a_rotaviruses Group a rotaviruses] and [http://en.wikipedia.org/wiki/Rotrh Rotrh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GZU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gzt\|3gzt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gzt\|3gzt]]</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=3gzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gzu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gzu RCSB], [http://www.ebi.ac.uk/pdbsum/3gzu 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=3gzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gzu OCA], [http://pdbe.org/3gzu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gzu RCSB], [http://www.ebi.ac.uk/pdbsum/3gzu PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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=3gzu ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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 3gzu" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rhesus rotavirus~~]]	+	[[Category: Group a rotaviruses]]
-	[[Category: ~~Rotavirus a~~]]	+	[[Category: Rotrh]]
	[[Category: Chen, J Z]]		[[Category: Chen, J Z]]
	[[Category: Grigorieff, N]]		[[Category: Grigorieff, N]]

OCA at 14:54, 24 December 2014

2014-12-24T14:54:48Z

←Older revision		Revision as of 14:54, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3gzu]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhesus_rotavirus Rhesus rotavirus] and [http://en.wikipedia.org/wiki/Rotavirus_a Rotavirus a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GZU FirstGlance]. <br>		<table><tr><td colspan='2'>[[3gzu]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhesus_rotavirus Rhesus rotavirus] and [http://en.wikipedia.org/wiki/Rotavirus_a Rotavirus a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GZU FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gzt\|3gzt]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gzt\|3gzt]]</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=3gzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gzu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gzu RCSB], [http://www.ebi.ac.uk/pdbsum/3gzu 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=3gzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gzu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gzu RCSB], [http://www.ebi.ac.uk/pdbsum/3gzu PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VP2_ROTW3 VP2_ROTW3]] 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. 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. VP2 is required for the replicase activity of VP1 polymerase. It probably plays a role in the coordination of packaging and genome replication by controlling the initiation of minus-strand synthesis. Binding to the polymerase VP1 presumably activates the autoinhibited VP1-RNA complex which will start the synthesis of the complementary minus-strand (By similarity). [[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 34:		Line 36:
	[[Category: Rhesus rotavirus]]		[[Category: Rhesus rotavirus]]
	[[Category: Rotavirus a]]		[[Category: Rotavirus a]]
-	[[Category: Chen, J Z.]]	+	[[Category: Chen, J Z]]
-	[[Category: Grigorieff, N.]]	+	[[Category: Grigorieff, N]]
-	[[Category: Harrison, S C.]]	+	[[Category: Harrison, S C]]
-	[[Category: Settembre, E C~~.]]~~	+	[[Category: Settembre, E C]]
-	~~[[Category: 7rp~~]]	+
	[[Category: Capsid protein]]		[[Category: Capsid protein]]
	[[Category: Core protein]]		[[Category: Core protein]]

OCA at 11:22, 29 September 2014

2014-09-29T11:22:15Z

←Older revision		Revision as of 11:22, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3gzu.~~png~~\|~~left~~\|200px]]	+	==VP7 recoated rotavirus DLP==
		+	<StructureSection load='3gzu' size='340' side='right' caption='[[3gzu]], [[Resolution\|resolution]] 3.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3gzu]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhesus_rotavirus Rhesus rotavirus] and [http://en.wikipedia.org/wiki/Rotavirus_a Rotavirus a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GZU FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gzt\|3gzt]]</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=3gzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gzu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gzu RCSB], [http://www.ebi.ac.uk/pdbsum/3gzu 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/gz/3gzu_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 ==
		+	Rotaviruses, major causes of childhood gastroenteritis, are nonenveloped, icosahedral particles with double-strand RNA genomes. By the use of electron cryomicroscopy and single-particle reconstruction, we have visualized a rotavirus particle comprising the inner capsid coated with the trimeric outer-layer protein, VP7, at a resolution (4 A) comparable with that of X-ray crystallography. We have traced the VP7 polypeptide chain, including parts not seen in its X-ray crystal structure. The 3 well-ordered, 30-residue, N-terminal "arms" of each VP7 trimer grip the underlying trimer of VP6, an inner-capsid protein. Structural differences between free and particle-bound VP7 and between free and VP7-coated inner capsids may regulate mRNA transcription and release. The Ca(2+)-stabilized VP7 intratrimer contact region, which presents important neutralizing epitopes, is unaltered upon capsid binding.

-	~~{{STRUCTURE_3gzu\| PDB=3gzu \| SCENE= }}~~	+	Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM.,Chen JZ, Settembre EC, Aoki ST, Zhang X, Bellamy AR, Dormitzer PR, Harrison SC, Grigorieff N Proc Natl Acad Sci U S A. 2009 Jun 30;106(26):10644-8. Epub 2009 Jun 1. PMID:19487668<ref>PMID:19487668</ref>

-	~~===VP7 recoated rotavirus DLP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19487668}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3gzu]] is a 15 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Rhesus_rotavirus Rhesus rotavirus] and [http://en.wikipedia.org/wiki/Rotavirus_a Rotavirus~~ a]. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3GZU OCA].~~	+

	==See Also==		==See Also==
	*[[Virus coat protein\|Virus coat protein]]		*[[Virus coat protein\|Virus coat protein]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019487668<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Rhesus rotavirus]]		[[Category: Rhesus rotavirus]]
	[[Category: Rotavirus a]]		[[Category: Rotavirus a]]

OCA: Protected "3gzu" [edit=sysop:move=sysop]

2012-10-20T06:34:18Z

Protected "3gzu" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:34, 20 October 2012