5vx9 - Revision history

OCA at 14:01, 4 October 2023

2023-10-04T14:01:43Z

←Older revision		Revision as of 14:01, 4 October 2023
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	<StructureSection load='5vx9' size='340' side='right'caption='[[5vx9]], [[Resolution\|resolution]] 1.82Å' scene=''>		<StructureSection load='5vx9' size='340' side='right'caption='[[5vx9]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vx9]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human_group_a_rotavirus~~ Human ~~group a~~ rotavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VX9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VX9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vx9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_rotavirus_A Human rotavirus A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VX9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.822Å</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=5vx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vx9 OCA], [~~http~~://pdbe.org/5vx9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vx9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vx9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vx9 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5vx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vx9 OCA], [https://pdbe.org/5vx9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vx9 RCSB], [https://www.ebi.ac.uk/pdbsum/5vx9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vx9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/D7F7M7_9REOV D7F7M7_9REOV]] Outer capsid protein VP5: Forms the spike "foot" and "body" and acts as a membrane permeabilization protein that mediates release of viral particles from endosomal compartments into the cytoplasm. During entry, the part of VP5 that protrudes from the virus folds back on itself and reorganizes from a local dimer to a trimer. This reorganization may be linked to membrane penetration by exposing VP5* hydrophobic region. In integrin-dependent strains, VP5* targets the integrin heterodimer ITGA2/ITGB1 for cell attachment.[SAAS:SAAS01043052]	+	[https://www.uniprot.org/uniprot/D7F7M7_9VIRU D7F7M7_9VIRU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5vx9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vx9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Human ~~group a~~ rotavirus]]	+	[[Category: Human rotavirus A]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hu, L]]	+	[[Category: Hu L]]
-	[[Category: Prasad~~, B V.Venkataram]]~~	+	[[Category: Venkataram Prasad BV]]
-	~~[[Category: Glycan]]~~	+
-	~~[[Category: Hbga]]~~	+
-	~~[[Category: Rotavirus]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 17:25, 11 December 2019

2019-12-11T17:25:03Z

←Older revision		Revision as of 17:25, 11 December 2019
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	==VP8* of P[6] Human Rotavirus RV3 in complex with LNFP1==		==VP8* of P[6] Human Rotavirus RV3 in complex with LNFP1==
-	<StructureSection load='5vx9' size='340' side='right' caption='[[5vx9]], [[Resolution\|resolution]] 1.82Å' scene=''>	+	<StructureSection load='5vx9' size='340' side='right'caption='[[5vx9]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vx9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VX9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VX9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vx9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_group_a_rotavirus Human group a rotavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VX9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VX9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5vx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vx9 OCA], [http://pdbe.org/5vx9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vx9 RCSB], [http://www.ebi.ac.uk/pdbsum/5vx9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vx9 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=5vx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vx9 OCA], [http://pdbe.org/5vx9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vx9 RCSB], [http://www.ebi.ac.uk/pdbsum/5vx9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vx9 ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human group a rotavirus]]
		+	[[Category: Large Structures]]
	[[Category: Hu, L]]		[[Category: Hu, L]]
	[[Category: Prasad, B V.Venkataram]]		[[Category: Prasad, B V.Venkataram]]

OCA at 07:26, 18 July 2018

2018-07-18T07:26:21Z

←Older revision		Revision as of 07:26, 18 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vx9 is ~~ON HOLD until Nov 28 2019~~	+	==VP8* of P[6] Human Rotavirus RV3 in complex with LNFP1==
		+	<StructureSection load='5vx9' size='340' side='right' caption='[[5vx9]], [[Resolution\|resolution]] 1.82Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5vx9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VX9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VX9 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5vx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vx9 OCA], [http://pdbe.org/5vx9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vx9 RCSB], [http://www.ebi.ac.uk/pdbsum/5vx9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vx9 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/D7F7M7_9REOV D7F7M7_9REOV]] Outer capsid protein VP5: Forms the spike "foot" and "body" and acts as a membrane permeabilization protein that mediates release of viral particles from endosomal compartments into the cytoplasm. During entry, the part of VP5 that protrudes from the virus folds back on itself and reorganizes from a local dimer to a trimer. This reorganization may be linked to membrane penetration by exposing VP5* hydrophobic region. In integrin-dependent strains, VP5* targets the integrin heterodimer ITGA2/ITGB1 for cell attachment.[SAAS:SAAS01043052]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Rotaviruses (RVs) cause life-threatening diarrhea in infants and children worldwide. Recent biochemical and epidemiological studies underscore the importance of histo-blood group antigens (HBGA) as both cell attachment and susceptibility factors for the globally dominant P[4], P[6], and P[8] genotypes of human RVs. How these genotypes interact with HBGA is not known. Here, our crystal structures of P[4] and a neonate-specific P[6] VP8s alone and in complex with H-type I HBGA reveal a unique glycan binding site that is conserved in the globally dominant genotypes and allows for the binding of ABH HBGAs, consistent with their prevalence. Remarkably, the VP8 of P[6] RVs isolated from neonates displays subtle structural changes in this binding site that may restrict its ability to bind branched glycans. This provides a structural basis for the age-restricted tropism of some P[6] RVs as developmentally regulated unbranched glycans are more abundant in the neonatal gut.

-	~~Authors: Hu~~, L~~., Venkataram Prasad~~, B.V.	+	Glycan recognition in globally dominant human rotaviruses.,Hu L, Sankaran B, Laucirica DR, Patil K, Salmen W, Ferreon ACM, Tsoi PS, Lasanajak Y, Smith DF, Ramani S, Atmar RL, Estes MK, Ferreon JC, Prasad BVV Nat Commun. 2018 Jul 6;9(1):2631. doi: 10.1038/s41467-018-05098-4. PMID:29980685<ref>PMID:29980685</ref>

-	Description: VP8* of ~~P[6] Human Rotavirus RV3 in complex with LNFP1~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5vx9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Hu, L]]		[[Category: Hu, L]]
-	[[Category: ~~Venkataram~~ Prasad, B.V]]	+	[[Category: Prasad, B V.Venkataram]]
		+	[[Category: Glycan]]
		+	[[Category: Hbga]]
		+	[[Category: Rotavirus]]
		+	[[Category: Viral protein]]

OCA at 04:27, 4 April 2018

2018-04-04T04:27:42Z

←Older revision		Revision as of 04:27, 4 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5vx9 is ON HOLD until ~~Paper Publication~~	+	The entry 5vx9 is ON HOLD until Nov 28 2019

	Authors: Hu, L., Venkataram Prasad, B.V.		Authors: Hu, L., Venkataram Prasad, B.V.

OCA: Protected "5vx9" [edit=sysop:move=sysop]

2017-09-27T14:15:55Z

Protected "5vx9" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:15, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5vx9 is ON HOLD until Paper Publication Authors: Hu, L., Venkataram Prasad, B.V. Description: VP8* of P[6] Human Rotavirus RV3 in complex with LNFP...

2017-09-27T14:15:54Z

New page: '''Unreleased structure''' The entry 5vx9 is ON HOLD until Paper Publication Authors: Hu, L., Venkataram Prasad, B.V. Description: VP8* of P[6] Human Rotavirus RV3 in complex with LNFP...

New page

'''Unreleased structure'''

The entry 5vx9 is ON HOLD until Paper Publication

Authors: Hu, L., Venkataram Prasad, B.V.

Description: VP8* of P[6] Human Rotavirus RV3 in complex with LNFP1
[[Category: Unreleased Structures]]
[[Category: Hu, L]]
[[Category: Venkataram Prasad, B.V]]