6pcu - Revision history

OCA at 07:27, 11 October 2023

OCA — Wed, 11 Oct 2023 07:27:03 GMT

←Older revision		Revision as of 07:27, 11 October 2023
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	<StructureSection load='6pcu' size='340' side='right'caption='[[6pcu]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='6pcu' size='340' side='right'caption='[[6pcu]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pcu]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Group_a_rotaviruses Group a rotaviruses~~] and [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PCU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6PCU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pcu]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Rotavirus_A Rotavirus A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PCU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PCU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.4Å</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=6pcu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pcu OCA], [~~http~~://pdbe.org/6pcu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6pcu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6pcu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6pcu ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6pcu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pcu OCA], [https://pdbe.org/6pcu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pcu RCSB], [https://www.ebi.ac.uk/pdbsum/6pcu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pcu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/Q2VE61_9REOV Q2VE61_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/Q2VE61_9VIRU Q2VE61_9VIRU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6pcu" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6pcu" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
		+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
		+	*[[3D structures of human antibody\|3D structures of human antibody]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Group a rotaviruses]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Hu, L]]~~	+	[[Category: Rotavirus A]]
-	~~[[Category: Prasad, B V.Venkataram]]~~	+	[[Category: Hu L]]
-	~~[[Category: Antibody]]~~	+	[[Category: Venkataram Prasad BV]]
-	[[Category: Rotavirus]]	+
-	[[Category: ~~Scfv~~]]	+
-	[[Category: ~~Viral protein]]~~	+
-	~~[[Category: Viral protein-immune system complex~~]]	+

OCA at 13:07, 25 December 2019

OCA — Wed, 25 Dec 2019 13:07:17 GMT

←Older revision		Revision as of 13:07, 25 December 2019
Line 3:		Line 3:
	<StructureSection load='6pcu' size='340' side='right'caption='[[6pcu]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='6pcu' size='340' side='right'caption='[[6pcu]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pcu]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Group_a_rotaviruses Group a rotaviruses] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PCU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PCU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pcu]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Group_a_rotaviruses Group a rotaviruses] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PCU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PCU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=GOL:GLYCEROL'>GOL</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=6pcu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pcu OCA], [http://pdbe.org/6pcu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pcu RCSB], [http://www.ebi.ac.uk/pdbsum/6pcu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pcu 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=6pcu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pcu OCA], [http://pdbe.org/6pcu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pcu RCSB], [http://www.ebi.ac.uk/pdbsum/6pcu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pcu ProSAT]</span></td></tr>

OCA at 12:23, 18 December 2019

OCA — Wed, 18 Dec 2019 12:23:36 GMT

←Older revision		Revision as of 12:23, 18 December 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6pcu is ~~ON HOLD until Paper~~ Publication	+	==VP8* of a G2P[4] human rotavirus in complex with scFv antibody 9==
		+	<StructureSection load='6pcu' size='340' side='right'caption='[[6pcu]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6pcu]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Group_a_rotaviruses Group a rotaviruses] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PCU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PCU FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6pcu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pcu OCA], [http://pdbe.org/6pcu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pcu RCSB], [http://www.ebi.ac.uk/pdbsum/6pcu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pcu ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q2VE61_9REOV Q2VE61_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 ==
		+	We previously generated 32 rotavirus-specific (RV-specific) recombinant monoclonal antibodies (mAbs) derived from B cells isolated from human intestinal resections. Twenty-four of these mAbs were specific for the VP8* fragment of RV VP4, and most (20 of 24) were non-neutralizing when tested in the conventional MA104 cell-based assay. We reexamined the ability of these mAbs to neutralize RVs in human intestinal epithelial cells including ileal enteroids and HT-29 cells. Most (18 of 20) of the "non-neutralizing" VP8* mAbs efficiently neutralized human RV in HT-29 cells or enteroids. Serum RV neutralization titers in adults and infants were significantly higher in HT-29 than MA104 cells and adsorption of these sera with recombinant VP8* lowered the neutralization titers in HT-29 but not MA104 cells. VP8* mAbs also protected suckling mice from diarrhea in an in vivo challenge model. X-ray crystallographic analysis of one VP8* mAb (mAb9) in complex with human RV VP8* revealed that the mAb interaction site was distinct from the human histo-blood group antigen binding site. Since MA104 cells are the most commonly used cell line to detect anti-RV neutralization activity, these findings suggest that prior vaccine and other studies of human RV neutralization responses may have underestimated the contribution of VP8* antibodies to the overall neutralization titer.

-	~~Authors~~:	+	Human VP8* mAbs neutralize rotavirus selectively in human intestinal epithelial cells.,Feng N, Hu L, Ding S, Sanyal M, Zhao B, Sankaran B, Ramani S, McNeal M, Yasukawa LL, Song Y, Prasad BVV, Greenberg HB J Clin Invest. 2019 Aug 12;130:3839-3851. doi: 10.1172/JCI128382. eCollection, 2019 Aug 12. PMID:31403468<ref>PMID:31403468</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6pcu" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Group a rotaviruses]]
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
		+	[[Category: Hu, L]]
		+	[[Category: Prasad, B V.Venkataram]]
		+	[[Category: Antibody]]
		+	[[Category: Rotavirus]]
		+	[[Category: Scfv]]
		+	[[Category: Viral protein]]
		+	[[Category: Viral protein-immune system complex]]

OCA: Protected "6pcu" [edit=sysop:move=sysop]

OCA — Wed, 26 Jun 2019 05:17:34 GMT

Protected "6pcu" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:17, 26 June 2019

OCA: New page: '''Unreleased structure''' The entry 6pcu is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 26 Jun 2019 05:17:33 GMT

New page: '''Unreleased structure''' The entry 6pcu is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6pcu is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]