4kte - Revision history

OCA at 09:12, 7 December 2022

OCA — Wed, 07 Dec 2022 09:12:42 GMT

←Older revision		Revision as of 09:12, 7 December 2022
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	<StructureSection load='4kte' size='340' side='right'caption='[[4kte]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='4kte' size='340' side='right'caption='[[4kte]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4kte]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Macmu Macmu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KTE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4KTE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4kte]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Macaca_mulatta Macaca mulatta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KTE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KTE 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" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~PCA~~:~~PYROGLUTAMIC~~+~~ACID~~'>~~PCA~~</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=4kte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kte OCA], [https://pdbe.org/4kte PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kte RCSB], [https://www.ebi.ac.uk/pdbsum/4kte PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kte ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ktd\|4ktd]]~~</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=4kte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kte OCA], [~~http~~://pdbe.org/4kte PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4kte RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4kte PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4kte ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Macmu~~]]	+	[[Category: Macaca mulatta]]
-	[[Category: Poulsen, C]]	+	[[Category: Poulsen C]]
-	[[Category: Stanfield, R]]	+	[[Category: Stanfield R]]
-	[[Category: Tran, K]]	+	[[Category: Tran K]]
-	[[Category: Wyatt~~, R T]]~~	+	[[Category: Wyatt RT]]
-	~~[[Category: Aids vaccine]]~~	+
-	~~[[Category: Antibody affinity]]~~	+
-	~~[[Category: Antibody specificity]]~~	+
-	~~[[Category: Fab fragment]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Vaccine elicited antibody~~]]	+

OCA at 10:04, 25 December 2019

OCA — Wed, 25 Dec 2019 10:04:02 GMT

←Older revision		Revision as of 10:04, 25 December 2019
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	==Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE148, from non-human primate==		==Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE148, from non-human primate==
-	<StructureSection load='4kte' size='340' side='right' caption='[[4kte]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='4kte' size='340' side='right'caption='[[4kte]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4kte]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Macmu Macmu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KTE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KTE FirstGlance]. <br>		<table><tr><td colspan='2'>[[4kte]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Macmu Macmu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KTE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KTE FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Macmu]]		[[Category: Macmu]]
	[[Category: Poulsen, C]]		[[Category: Poulsen, C]]

OCA at 07:17, 23 December 2016

OCA — Fri, 23 Dec 2016 07:17:06 GMT

←Older revision		Revision as of 07:17, 23 December 2016
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		+
	==Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE148, from non-human primate==		==Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE148, from non-human primate==
	<StructureSection load='4kte' size='340' side='right' caption='[[4kte]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='4kte' size='340' side='right' caption='[[4kte]], [[Resolution\|resolution]] 1.80Å' scene=''>
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	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ktd\|4ktd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ktd\|4ktd]]</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=4kte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kte OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kte RCSB], [http://www.ebi.ac.uk/pdbsum/4kte 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=4kte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kte OCA], [http://pdbe.org/4kte PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kte RCSB], [http://www.ebi.ac.uk/pdbsum/4kte PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kte ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 4kte" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:13, 15 February 2015

OCA — Sun, 15 Feb 2015 07:13:02 GMT

←Older revision		Revision as of 07:13, 15 February 2015
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-	~~{{STRUCTURE_4kte\| PDB=4kte \| SCENE= }}~~	+	==Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE148, from non-human primate==
-	===Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE148, from non-human primate===	+	<StructureSection load='4kte' size='340' side='right' caption='[[4kte]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24550318}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4kte]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Macmu Macmu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KTE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KTE 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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ktd\|4ktd]]</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=4kte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kte OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kte RCSB], [http://www.ebi.ac.uk/pdbsum/4kte PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	HIV-1 neutralization requires Ab accessibility to the functional envelope glycoprotein (Env) spike. We recently reported the isolation of previously unidentified vaccine-elicited, CD4 binding site (CD4bs)-directed mAbs from rhesus macaques immunized with soluble Env trimers, indicating that this region is immunogenic in the context of subunit vaccination. To elucidate the interaction of the trimer-elicited mAbs with gp120 and their insufficient interaction with the HIV-1 primary isolate spike, we crystallized the Fab fragments of two mAbs, GE136 and GE148. Alanine scanning of their complementarity-determining regions, coupled with epitope scanning of their epitopes on gp120, revealed putative contact residues at the Ab/gp120 interface. Docking of the GE136 and GE148 Fabs to gp120, coupled with EM reconstructions of these nonbroadly neutralizing mAbs (non-bNAbs) binding to gp120 monomers and EM modeling to well-ordered trimers, suggested Ab approach to the CD4bs by a vertical angle of access relative to the more lateral mode of interaction used by the CD4bs-directed bNAbs VRC01 and PGV04. Fitting the structures into the available cryo-EM native spike density indicated clashes between these two vaccine-elicited mAbs and the topside variable region spike cap, whereas the bNAbs duck under this quaternary shield to access the CD4bs effectively on primary HIV isolates. These results provide a structural basis for the limited neutralizing breadth observed by current vaccine-induced, CD4bs-directed Abs and highlight the need for better ordered trimer immunogens. The analysis presented here therefore provides valuable information to guide HIV-1 vaccine immunogen redesign.

-	~~==About this Structure==~~	+	Vaccine-elicited primate antibodies use a distinct approach to the HIV-1 primary receptor binding site informing vaccine redesign.,Tran K, Poulsen C, Guenaga J, de Val Alda N, Wilson R, Sundling C, Li Y, Stanfield RL, Wilson IA, Ward AB, Karlsson Hedestam GB, Wyatt RT Proc Natl Acad Sci U S A. 2014 Feb 18;111(7):E738-47. doi:, 10.1073/pnas.1319512111. Epub 2014 Feb 3. PMID:24550318<ref>PMID:24550318</ref>
-	~~[[4kte]] is~~ a ~~2 chain structure~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4KTE OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024550318</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Poulsen, C.]]	+	== References ==
-	[[Category: Stanfield, R.]]	+	<references/>
-	[[Category: Tran, K.]]	+	__TOC__
-	[[Category: Wyatt, R T.]]	+	</StructureSection>
		+	[[Category: Macmu]]
		+	[[Category: Poulsen, C]]
		+	[[Category: Stanfield, R]]
		+	[[Category: Tran, K]]
		+	[[Category: Wyatt, R T]]
	[[Category: Aids vaccine]]		[[Category: Aids vaccine]]
	[[Category: Antibody affinity]]		[[Category: Antibody affinity]]

OCA at 09:04, 19 March 2014

OCA — Wed, 19 Mar 2014 09:04:40 GMT

←Older revision		Revision as of 09:04, 19 March 2014
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	{{STRUCTURE_4kte\| PDB=4kte \| SCENE= }}		{{STRUCTURE_4kte\| PDB=4kte \| SCENE= }}
	===Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE148, from non-human primate===		===Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE148, from non-human primate===
		+	{{ABSTRACT_PUBMED_24550318}}

	==About this Structure==		==About this Structure==
	[[4kte]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KTE OCA].		[[4kte]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KTE OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:024550318</ref><references group="xtra"/><references/>
	[[Category: Poulsen, C.]]		[[Category: Poulsen, C.]]
	[[Category: Stanfield, R.]]		[[Category: Stanfield, R.]]

OCA at 11:33, 5 February 2014

OCA — Wed, 05 Feb 2014 11:33:53 GMT

←Older revision		Revision as of 11:33, 5 February 2014
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-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4kte\| PDB=4kte \| SCENE= }}
		+	===Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE148, from non-human primate===

-	~~The entry~~ 4kte is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[4kte]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KTE OCA].
-	~~Authors~~: Poulsen, C.~~, Tran, K.,~~ Stanfield, R., Wyatt, R.T.	+	[[Category: Poulsen, C.]]
-		+	[[Category: Stanfield, R.]]
-	~~Description~~: Fab fragment ~~of HIV vaccine-~~elicited ~~CD4bs-directed~~ antibody~~, GE148, from non-human primate~~	+	[[Category: Tran, K.]]
		+	[[Category: Wyatt, R T.]]
		+	[[Category: Aids vaccine]]
		+	[[Category: Antibody affinity]]
		+	[[Category: Antibody specificity]]
		+	[[Category: Fab fragment]]
		+	[[Category: Immune system]]
		+	[[Category: Vaccine elicited antibody]]

OCA: Protected "4kte" [edit=sysop:move=sysop]

OCA — Wed, 19 Jun 2013 12:00:51 GMT

Protected "4kte" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:00, 19 June 2013

OCA: New page: '''Unreleased structure''' The entry 4kte is ON HOLD until Paper Publication Authors: Poulsen, C., Tran, K., Stanfield, R., Wyatt, R.T. Description: Fab fragment of HIV vaccine-elicite...

OCA — Wed, 19 Jun 2013 12:00:50 GMT

New page: '''Unreleased structure''' The entry 4kte is ON HOLD until Paper Publication Authors: Poulsen, C., Tran, K., Stanfield, R., Wyatt, R.T. Description: Fab fragment of HIV vaccine-elicite...

New page

'''Unreleased structure'''

The entry 4kte is ON HOLD until Paper Publication

Authors: Poulsen, C., Tran, K., Stanfield, R., Wyatt, R.T.

Description: Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE148, from non-human primate