1slq - Revision history

OCA at 08:32, 14 February 2024

OCA — Wed, 14 Feb 2024 08:32:07 GMT

←Older revision		Revision as of 08:32, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1slq' size='340' side='right'caption='[[1slq]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='1slq' size='340' side='right'caption='[[1slq]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1slq]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SLQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1slq]] is a 6 chain structure with sequence from [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=1SLQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SLQ 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;'~~>~~[[1kqr\|1kqr]]~~, [[~~1kri~~\|~~1kri~~]]~~</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]] 3.2Å</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=1slq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slq OCA], [https://pdbe.org/1slq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1slq RCSB], [https://www.ebi.ac.uk/pdbsum/1slq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1slq 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=1slq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slq OCA], [https://pdbe.org/1slq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1slq RCSB], [https://www.ebi.ac.uk/pdbsum/1slq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1slq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/VP4_ROTRH VP4_ROTRH]] Spike-forming protein that mediates virion attachment to the host epithelial cell receptors and plays a major role in cell penetration, determination of host range restriction and virulence. It is subsequently lost, together with VP7, following virus entry into the host cell. Rotavirus attachment and entry into the host cell probably involves multiple sequential contacts between the outer capsid proteins VP4 and VP7, and the cell receptors. In sialic acid-dependent and/or integrin-dependent strains, VP4 seems to essentially target sialic acid and/or the integrin heterodimer ITGA2/ITGB1.<ref>PMID:20375171</ref> Outer capsid protein VP5: forms the spike "foot" and "body". Acts as a membrane permeabilization protein that mediates release of viral particles from endosomal compartments into the cytoplasm. In integrin-dependent strains, VP5 targets the integrin heterodimer ITGA2/ITGB1 for cell attachment.<ref>PMID:20375171</ref> VP8* forms the head of the spikes. It is the viral hemagglutinin and an important target of neutralizing antibodies. In sialic acid-dependent strains, VP8* binds to host cell sialic acid, most probably a ganglioside, providing the initial contact.<ref>PMID:20375171</ref>	+	[https://www.uniprot.org/uniprot/VP4_ROTRH VP4_ROTRH] Spike-forming protein that mediates virion attachment to the host epithelial cell receptors and plays a major role in cell penetration, determination of host range restriction and virulence. It is subsequently lost, together with VP7, following virus entry into the host cell. Rotavirus attachment and entry into the host cell probably involves multiple sequential contacts between the outer capsid proteins VP4 and VP7, and the cell receptors. In sialic acid-dependent and/or integrin-dependent strains, VP4 seems to essentially target sialic acid and/or the integrin heterodimer ITGA2/ITGB1.<ref>PMID:20375171</ref> Outer capsid protein VP5: forms the spike "foot" and "body". Acts as a membrane permeabilization protein that mediates release of viral particles from endosomal compartments into the cytoplasm. In integrin-dependent strains, VP5 targets the integrin heterodimer ITGA2/ITGB1 for cell attachment.<ref>PMID:20375171</ref> VP8* forms the head of the spikes. It is the viral hemagglutinin and an important target of neutralizing antibodies. In sialic acid-dependent strains, VP8* binds to host cell sialic acid, most probably a ganglioside, providing the initial contact.<ref>PMID:20375171</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 19:
	</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=1slq 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=1slq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Non-enveloped virus particles (those that lack a lipid-bilayer membrane) must breach the membrane of a target host cell to gain access to its cytoplasm. So far, the molecular mechanism of this membrane penetration step has resisted structural analysis. The spike protein VP4 is a principal component in the entry apparatus of rotavirus, a non-enveloped virus that causes gastroenteritis and kills 440,000 children each year. Trypsin cleavage of VP4 primes the virus for entry by triggering a rearrangement that rigidifies the VP4 spikes. We have determined the crystal structure, at 3.2 A resolution, of the main part of VP4 that projects from the virion. The crystal structure reveals a coiled-coil stabilized trimer. Comparison of this structure with the two-fold clustered VP4 spikes in a approximately 12 A resolution image reconstruction from electron cryomicroscopy of trypsin-primed virions shows that VP4 also undergoes a second rearrangement, in which the oligomer reorganizes and each subunit folds back on itself, translocating a potential membrane-interaction peptide from one end of the spike to the other. This rearrangement resembles the conformational transitions of membrane fusion proteins of enveloped viruses.
-
-	Structural rearrangements in the membrane penetration protein of a non-enveloped virus.,Dormitzer PR, Nason EB, Prasad BV, Harrison SC Nature. 2004 Aug 26;430(7003):1053-8. PMID:15329727<ref>PMID:15329727</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1slq" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Dormitzer, P R~~]]	+	[[Category: Simian rotavirus A strain RRV]]
-	[[Category: ~~Harrison, S C~~]]	+	[[Category: Dormitzer PR]]
-	[[Category: ~~Nason, E B~~]]	+	[[Category: Harrison SC]]
-	[[Category: ~~Prasad, B V.V~~]]	+	[[Category: Nason EB]]
-	[[Category: ~~Alpha helical triple coiled-coil]]~~	+	[[Category: Prasad BVV]]
-	~~[[Category: Beta sandwich]]~~	+
-	~~[[Category: Greek key]]~~	+
-	~~[[Category: Membrane penetration protein]]~~	+
-	~~[[Category: Non-enveloped virus]]~~	+
-	~~[[Category: Spike protein]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 11:29, 30 March 2022

OCA — Wed, 30 Mar 2022 11:29:54 GMT

←Older revision		Revision as of 11:29, 30 March 2022
Line 3:		Line 3:
	<StructureSection load='1slq' size='340' side='right'caption='[[1slq]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='1slq' size='340' side='right'caption='[[1slq]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1slq]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1SLQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1slq]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SLQ FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kqr\|1kqr]], [[1kri\|1kri]]</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;'>[[1kqr\|1kqr]], [[1kri\|1kri]]</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=1slq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slq OCA], [~~http~~://pdbe.org/1slq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1slq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1slq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1slq 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=1slq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slq OCA], [https://pdbe.org/1slq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1slq RCSB], [https://www.ebi.ac.uk/pdbsum/1slq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1slq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/VP4_ROTRH VP4_ROTRH]] Spike-forming protein that mediates virion attachment to the host epithelial cell receptors and plays a major role in cell penetration, determination of host range restriction and virulence. It is subsequently lost, together with VP7, following virus entry into the host cell. Rotavirus attachment and entry into the host cell probably involves multiple sequential contacts between the outer capsid proteins VP4 and VP7, and the cell receptors. In sialic acid-dependent and/or integrin-dependent strains, VP4 seems to essentially target sialic acid and/or the integrin heterodimer ITGA2/ITGB1.<ref>PMID:20375171</ref> Outer capsid protein VP5: forms the spike "foot" and "body". Acts as a membrane permeabilization protein that mediates release of viral particles from endosomal compartments into the cytoplasm. In integrin-dependent strains, VP5 targets the integrin heterodimer ITGA2/ITGB1 for cell attachment.<ref>PMID:20375171</ref> VP8* forms the head of the spikes. It is the viral hemagglutinin and an important target of neutralizing antibodies. In sialic acid-dependent strains, VP8* binds to host cell sialic acid, most probably a ganglioside, providing the initial contact.<ref>PMID:20375171</ref>	+	[[https://www.uniprot.org/uniprot/VP4_ROTRH VP4_ROTRH]] Spike-forming protein that mediates virion attachment to the host epithelial cell receptors and plays a major role in cell penetration, determination of host range restriction and virulence. It is subsequently lost, together with VP7, following virus entry into the host cell. Rotavirus attachment and entry into the host cell probably involves multiple sequential contacts between the outer capsid proteins VP4 and VP7, and the cell receptors. In sialic acid-dependent and/or integrin-dependent strains, VP4 seems to essentially target sialic acid and/or the integrin heterodimer ITGA2/ITGB1.<ref>PMID:20375171</ref> Outer capsid protein VP5: forms the spike "foot" and "body". Acts as a membrane permeabilization protein that mediates release of viral particles from endosomal compartments into the cytoplasm. In integrin-dependent strains, VP5 targets the integrin heterodimer ITGA2/ITGB1 for cell attachment.<ref>PMID:20375171</ref> VP8* forms the head of the spikes. It is the viral hemagglutinin and an important target of neutralizing antibodies. In sialic acid-dependent strains, VP8* binds to host cell sialic acid, most probably a ganglioside, providing the initial contact.<ref>PMID:20375171</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:34, 25 June 2020

OCA — Thu, 25 Jun 2020 07:34:31 GMT

←Older revision		Revision as of 07:34, 25 June 2020
Line 1:		Line 1:

	==Crystal structure of the trimeric state of the rhesus rotavirus VP4 membrane interaction domain, VP5CT==		==Crystal structure of the trimeric state of the rhesus rotavirus VP4 membrane interaction domain, VP5CT==
-	<StructureSection load='1slq' size='340' side='right' caption='[[1slq]], [[Resolution\|resolution]] 3.20Å' scene=''>	+	<StructureSection load='1slq' size='340' side='right'caption='[[1slq]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1slq]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLQ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1SLQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1slq]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1SLQ FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kqr\|1kqr]], [[1kri\|1kri]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kqr\|1kqr]], [[1kri\|1kri]]</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=1slq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slq OCA], [http://pdbe.org/1slq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1slq RCSB], [http://www.ebi.ac.uk/pdbsum/1slq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1slq 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=1slq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slq OCA], [http://pdbe.org/1slq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1slq RCSB], [http://www.ebi.ac.uk/pdbsum/1slq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1slq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Virus coat ~~protein~~\|Virus coat ~~protein~~]]	+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Dormitzer, P R]]		[[Category: Dormitzer, P R]]
	[[Category: Harrison, S C]]		[[Category: Harrison, S C]]

OCA at 21:05, 19 September 2018

OCA — Wed, 19 Sep 2018 21:05:49 GMT

←Older revision		Revision as of 21:05, 19 September 2018
Line 1:		Line 1:
		+
	==Crystal structure of the trimeric state of the rhesus rotavirus VP4 membrane interaction domain, VP5CT==		==Crystal structure of the trimeric state of the rhesus rotavirus VP4 membrane interaction domain, VP5CT==
	<StructureSection load='1slq' size='340' side='right' caption='[[1slq]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='1slq' size='340' side='right' caption='[[1slq]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1slq]] is a 6 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Rotrh Rotrh]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SLQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1slq]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SLQ FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kqr\|1kqr]], [[1kri\|1kri]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kqr\|1kqr]], [[1kri\|1kri]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gene segment 4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10969 ROTRH])</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=1slq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slq OCA], [http://pdbe.org/1slq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1slq RCSB], [http://www.ebi.ac.uk/pdbsum/1slq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1slq ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1slq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slq OCA], [http://pdbe.org/1slq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1slq RCSB], [http://www.ebi.ac.uk/pdbsum/1slq PDBsum]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sl/1slq_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sl/1slq_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=1slq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[~~VP4~~\|~~VP4~~]]	+	*[[Virus coat protein\|Virus coat protein]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Rotrh]]
	[[Category: Dormitzer, P R]]		[[Category: Dormitzer, P R]]
	[[Category: Harrison, S C]]		[[Category: Harrison, S C]]

OCA at 13:55, 11 September 2015

OCA — Fri, 11 Sep 2015 13:55:09 GMT

←Older revision		Revision as of 13:55, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1slq' size='340' side='right' caption='[[1slq]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='1slq' size='340' side='right' caption='[[1slq]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1slq]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rhesus_rotavirus Rhesus rotavirus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SLQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1slq]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Rotrh Rotrh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SLQ FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kqr\|1kqr]], [[1kri\|1kri]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kqr\|1kqr]], [[1kri\|1kri]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gene segment 4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10969 ~~Rhesus rotavirus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gene segment 4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10969 ROTRH])</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=1slq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1slq RCSB], [http://www.ebi.ac.uk/pdbsum/1slq 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=1slq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slq OCA], [http://pdbe.org/1slq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1slq RCSB], [http://www.ebi.ac.uk/pdbsum/1slq 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 1slq" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[VP4\|VP4]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rhesus rotavirus~~]]	+	[[Category: Rotrh]]
	[[Category: Dormitzer, P R]]		[[Category: Dormitzer, P R]]
	[[Category: Harrison, S C]]		[[Category: Harrison, S C]]

OCA at 17:21, 25 December 2014

OCA — Thu, 25 Dec 2014 17:21:58 GMT

←Older revision		Revision as of 17:21, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1slq]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhesus_rotavirus Rhesus rotavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SLQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1slq]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhesus_rotavirus Rhesus rotavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SLQ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kqr\|1kqr]], [[1kri\|1kri]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kqr\|1kqr]], [[1kri\|1kri]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gene segment 4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10969 Rhesus rotavirus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gene segment 4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10969 Rhesus 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=1slq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1slq RCSB], [http://www.ebi.ac.uk/pdbsum/1slq 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=1slq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1slq RCSB], [http://www.ebi.ac.uk/pdbsum/1slq PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VP4_ROTRH VP4_ROTRH]] Spike-forming protein that mediates virion attachment to the host epithelial cell receptors and plays a major role in cell penetration, determination of host range restriction and virulence. It is subsequently lost, together with VP7, following virus entry into the host cell. Rotavirus attachment and entry into the host cell probably involves multiple sequential contacts between the outer capsid proteins VP4 and VP7, and the cell receptors. In sialic acid-dependent and/or integrin-dependent strains, VP4 seems to essentially target sialic acid and/or the integrin heterodimer ITGA2/ITGB1.<ref>PMID:20375171</ref> Outer capsid protein VP5: forms the spike "foot" and "body". Acts as a membrane permeabilization protein that mediates release of viral particles from endosomal compartments into the cytoplasm. In integrin-dependent strains, VP5 targets the integrin heterodimer ITGA2/ITGB1 for cell attachment.<ref>PMID:20375171</ref> VP8* forms the head of the spikes. It is the viral hemagglutinin and an important target of neutralizing antibodies. In sialic acid-dependent strains, VP8* binds to host cell sialic acid, most probably a ganglioside, providing the initial contact.<ref>PMID:20375171</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Rhesus rotavirus]]		[[Category: Rhesus rotavirus]]
-	[[Category: Dormitzer, P R.]]	+	[[Category: Dormitzer, P R]]
-	[[Category: Harrison, S C.]]	+	[[Category: Harrison, S C]]
-	[[Category: Nason, E B.]]	+	[[Category: Nason, E B]]
-	[[Category: Prasad, B V.V.]]	+	[[Category: Prasad, B V.V]]
	[[Category: Alpha helical triple coiled-coil]]		[[Category: Alpha helical triple coiled-coil]]
	[[Category: Beta sandwich]]		[[Category: Beta sandwich]]

OCA at 16:05, 29 September 2014

OCA — Mon, 29 Sep 2014 16:05:54 GMT

←Older revision		Revision as of 16:05, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1slq.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the trimeric state of the rhesus rotavirus VP4 membrane interaction domain, VP5CT==
		+	<StructureSection load='1slq' size='340' side='right' caption='[[1slq]], [[Resolution\|resolution]] 3.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1slq]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhesus_rotavirus Rhesus rotavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SLQ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kqr\|1kqr]], [[1kri\|1kri]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gene segment 4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10969 Rhesus 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=1slq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1slq RCSB], [http://www.ebi.ac.uk/pdbsum/1slq 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/sl/1slq_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 ==
		+	Non-enveloped virus particles (those that lack a lipid-bilayer membrane) must breach the membrane of a target host cell to gain access to its cytoplasm. So far, the molecular mechanism of this membrane penetration step has resisted structural analysis. The spike protein VP4 is a principal component in the entry apparatus of rotavirus, a non-enveloped virus that causes gastroenteritis and kills 440,000 children each year. Trypsin cleavage of VP4 primes the virus for entry by triggering a rearrangement that rigidifies the VP4 spikes. We have determined the crystal structure, at 3.2 A resolution, of the main part of VP4 that projects from the virion. The crystal structure reveals a coiled-coil stabilized trimer. Comparison of this structure with the two-fold clustered VP4 spikes in a approximately 12 A resolution image reconstruction from electron cryomicroscopy of trypsin-primed virions shows that VP4 also undergoes a second rearrangement, in which the oligomer reorganizes and each subunit folds back on itself, translocating a potential membrane-interaction peptide from one end of the spike to the other. This rearrangement resembles the conformational transitions of membrane fusion proteins of enveloped viruses.

-	~~{{STRUCTURE_1slq\| PDB=1slq \| SCENE= }}~~	+	Structural rearrangements in the membrane penetration protein of a non-enveloped virus.,Dormitzer PR, Nason EB, Prasad BV, Harrison SC Nature. 2004 Aug 26;430(7003):1053-8. PMID:15329727<ref>PMID:15329727</ref>

-	~~===Crystal structure~~ of the ~~trimeric state of the rhesus rotavirus VP4 membrane interaction domain, VP5CT===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15329727}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1slq]] is a 6 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rhesus_rotavirus Rhesus rotavirus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1SLQ OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015329727<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Rhesus rotavirus]]		[[Category: Rhesus rotavirus]]
	[[Category: Dormitzer, P R.]]		[[Category: Dormitzer, P R.]]

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

OCA — Fri, 04 Jan 2013 10:33:56 GMT

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

←Older revision

Revision as of 10:33, 4 January 2013

OCA at 10:33, 4 January 2013

OCA — Fri, 04 Jan 2013 10:33:53 GMT

←Older revision		Revision as of 10:33, 4 January 2013
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-	{{Seed}}
	[[Image:1slq.png\|left\|200px]]		[[Image:1slq.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1slq", 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_1slq\| PDB=1slq \| SCENE= }}		{{STRUCTURE_1slq\| PDB=1slq \| SCENE= }}

	===Crystal structure of the trimeric state of the rhesus rotavirus VP4 membrane interaction domain, VP5CT===		===Crystal structure of the trimeric state of the rhesus rotavirus VP4 membrane interaction domain, VP5CT===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15329727}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15329727 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15329727}}		{{ABSTRACT_PUBMED_15329727}}

	==About this Structure==		==About this Structure==
-	~~1SLQ~~ is a 6 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Rhesus_rotavirus Rhesus rotavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLQ OCA].	+	[[1slq]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhesus_rotavirus Rhesus rotavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLQ OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15329727~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015329727</ref><references group="xtra"/>
	[[Category: Rhesus rotavirus]]		[[Category: Rhesus rotavirus]]
	[[Category: Dormitzer, P R.]]		[[Category: Dormitzer, P R.]]
Line 35:		Line 23:
	[[Category: Non-enveloped virus]]		[[Category: Non-enveloped virus]]
	[[Category: Spike protein]]		[[Category: Spike protein]]
-		+	[[Category: Viral protein]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Wed Feb 18 00:04:02 2009''~~	+

OCA at 22:04, 17 February 2009

OCA — Tue, 17 Feb 2009 22:04:04 GMT

←Older revision		Revision as of 22:04, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1SLQ is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Rhesus_rotavirus Rhesus rotavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLQ OCA].	+	1SLQ is a 6 chains structure of sequences from [http://en.wikipedia.org/wiki/Rhesus_rotavirus Rhesus rotavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLQ OCA].

	==Reference==		==Reference==
-	~~Structural rearrangements in the membrane penetration protein of a non-enveloped virus., Dormitzer PR, Nason EB, Prasad BV, Harrison SC, Nature. 2004 Aug 26;430(7003):1053-8.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15329727 15329727]~~	+	<ref group="xtra">PMID:15329727</ref><references group="xtra"/>
	[[Category: Rhesus rotavirus]]		[[Category: Rhesus rotavirus]]
-	[[Category: Single protein]]
	[[Category: Dormitzer, P R.]]		[[Category: Dormitzer, P R.]]
	[[Category: Harrison, S C.]]		[[Category: Harrison, S C.]]
Line 37:		Line 36:
	[[Category: Spike protein]]		[[Category: Spike protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 07~~:22:~~45 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:04:02 2009''