5i8e - Revision history

OCA at 08:26, 23 August 2023

OCA — Wed, 23 Aug 2023 08:26:35 GMT

←Older revision		Revision as of 08:26, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='5i8e' size='340' side='right'caption='[[5i8e]], [[Resolution\|resolution]] 2.66Å' scene=''>		<StructureSection load='5i8e' size='340' side='right'caption='[[5i8e]], [[Resolution\|resolution]] 2.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i8e]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I8E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5I8E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i8e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I8E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I8E 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='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.655Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i8c\|5i8c]]~~, [[~~5i8h~~\|~~5i8h~~]]</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='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~IGHG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN])~~</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=5i8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8e OCA], [https://pdbe.org/5i8e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i8e RCSB], [https://www.ebi.ac.uk/pdbsum/5i8e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8e 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=5i8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8e OCA], [~~http~~://pdbe.org/5i8e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5i8e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5i8e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8e ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kwong~~, P D~~]]	+	[[Category: Kwong PD]]
-	[[Category: Liu, K]]	+	[[Category: Liu K]]
-	[[Category: Xu, K]]	+	[[Category: Xu K]]
-	[[Category: Zhou, T]]	+	[[Category: Zhou T]]
-	~~[[Category: Antibody]]~~	+
-	~~[[Category: Envelope]]~~	+
-	~~[[Category: Fusion peptide]]~~	+
-	~~[[Category: Hiv-1]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Neutralizing]]~~	+
-	~~[[Category: Trimer~~]]	+

OCA at 16:16, 11 December 2019

OCA — Wed, 11 Dec 2019 16:16:26 GMT

←Older revision		Revision as of 16:16, 11 December 2019
Line 1:		Line 1:

	==Crystal Structure of Broadly Neutralizing HIV-1 Fusion Peptide-Targeting Antibody VRC34.01 Fab==		==Crystal Structure of Broadly Neutralizing HIV-1 Fusion Peptide-Targeting Antibody VRC34.01 Fab==
-	<StructureSection load='5i8e' size='340' side='right' caption='[[5i8e]], [[Resolution\|resolution]] 2.66Å' scene=''>	+	<StructureSection load='5i8e' size='340' side='right'caption='[[5i8e]], [[Resolution\|resolution]] 2.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i8e]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I8E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I8E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i8e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I8E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I8E 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">[[5i8c\|5i8c]], [[5i8h\|5i8h]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i8c\|5i8c]], [[5i8h\|5i8h]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IGHG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5i8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8e OCA], [http://pdbe.org/5i8e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i8e RCSB], [http://www.ebi.ac.uk/pdbsum/5i8e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8e 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=5i8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8e OCA], [http://pdbe.org/5i8e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i8e RCSB], [http://www.ebi.ac.uk/pdbsum/5i8e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8e ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Kwong, P D]]		[[Category: Kwong, P D]]
	[[Category: Liu, K]]		[[Category: Liu, K]]

OCA at 04:39, 21 September 2017

OCA — Thu, 21 Sep 2017 04:39:55 GMT

←Older revision		Revision as of 04:39, 21 September 2017
Line 6:		Line 6:
	</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">[[5i8c\|5i8c]], [[5i8h\|5i8h]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i8c\|5i8c]], [[5i8h\|5i8h]]</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=5i8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8e OCA], [http://pdbe.org/5i8e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i8e RCSB], [http://www.ebi.ac.uk/pdbsum/5i8e 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=5i8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8e OCA], [http://pdbe.org/5i8e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i8e RCSB], [http://www.ebi.ac.uk/pdbsum/5i8e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8e ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:00, 1 June 2016

OCA — Wed, 01 Jun 2016 23:00:21 GMT

←Older revision		Revision as of 23:00, 1 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5i8e is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of Broadly Neutralizing HIV-1 Fusion Peptide-Targeting Antibody VRC34.01 Fab==
		+	<StructureSection load='5i8e' size='340' side='right' caption='[[5i8e]], [[Resolution\|resolution]] 2.66Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5i8e]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I8E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I8E 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>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i8c\|5i8c]], [[5i8h\|5i8h]]</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=5i8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8e OCA], [http://pdbe.org/5i8e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i8e RCSB], [http://www.ebi.ac.uk/pdbsum/5i8e PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The HIV-1 fusion peptide, comprising 15 to 20 hydrophobic residues at the N terminus of the Env-gp41 subunit, is a critical component of the virus-cell entry machinery. Here, we report the identification of a neutralizing antibody, N123-VRC34.01, which targets the fusion peptide and blocks viral entry by inhibiting conformational changes in gp120 and gp41 subunits of Env required for entry. Crystal structures of N123-VRC34.01 liganded to the fusion peptide, and to the full Env trimer, revealed an epitope consisting of the N-terminal eight residues of the gp41 fusion peptide and glycan N88 of gp120, and molecular dynamics showed that the N-terminal portion of the fusion peptide can be solvent-exposed. These results reveal the fusion peptide to be a neutralizing antibody epitope and thus a target for vaccine design.

-	~~Authors: Xu~~, K., Zhou, T., Liu, K., Kwong, P.D.	+	Fusion peptide of HIV-1 as a site of vulnerability to neutralizing antibody.,Kong R, Xu K, Zhou T, Acharya P, Lemmin T, Liu K, Ozorowski G, Soto C, Taft JD, Bailer RT, Cale EM, Chen L, Choi CW, Chuang GY, Doria-Rose NA, Druz A, Georgiev IS, Gorman J, Huang J, Joyce MG, Louder MK, Ma X, McKee K, O'Dell S, Pancera M, Yang Y, Blanchard SC, Mothes W, Burton DR, Koff WC, Connors M, Ward AB, Kwong PD, Mascola JR Science. 2016 May 13;352(6287):828-33. doi: 10.1126/science.aae0474. PMID:27174988<ref>PMID:27174988</ref>

-	~~Description: Crystal Structure~~ of ~~Broadly Neutralizing HIV~~-~~1 Fusion Peptide~~-~~Targeting Antibody VRC34.01 Fab~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: Kwong, P.D]]	+	<div class="pdbe-citations 5i8e" style="background-color:#fffaf0;"></div>
-	~~[[Category: Zhou, T]]~~	+	== References ==
-	~~[[Category: Xu, K~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kwong, P D]]
	[[Category: Liu, K]]		[[Category: Liu, K]]
		+	[[Category: Xu, K]]
		+	[[Category: Zhou, T]]
		+	[[Category: Antibody]]
		+	[[Category: Envelope]]
		+	[[Category: Fusion peptide]]
		+	[[Category: Hiv-1]]
		+	[[Category: Immune system]]
		+	[[Category: Neutralizing]]
		+	[[Category: Trimer]]

OCA at 13:31, 2 March 2016

OCA — Wed, 02 Mar 2016 13:31:06 GMT

←Older revision		Revision as of 13:31, 2 March 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5i8e is ON HOLD	+	The entry 5i8e is ON HOLD until Paper Publication

	Authors: Xu, K., Zhou, T., Liu, K., Kwong, P.D.		Authors: Xu, K., Zhou, T., Liu, K., Kwong, P.D.

OCA: Protected "5i8e" [edit=sysop:move=sysop]

OCA — Fri, 26 Feb 2016 16:58:45 GMT

Protected "5i8e" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:58, 26 February 2016

OCA: New page: '''Unreleased structure''' The entry 5i8e is ON HOLD Authors: Xu, K., Zhou, T., Liu, K., Kwong, P.D. Description: Crystal Structure of Broadly Neutralizing HIV-1 Fusion Peptide-Targeti...

OCA — Fri, 26 Feb 2016 16:58:44 GMT

New page: '''Unreleased structure''' The entry 5i8e is ON HOLD Authors: Xu, K., Zhou, T., Liu, K., Kwong, P.D. Description: Crystal Structure of Broadly Neutralizing HIV-1 Fusion Peptide-Targeti...

New page

'''Unreleased structure'''

The entry 5i8e is ON HOLD

Authors: Xu, K., Zhou, T., Liu, K., Kwong, P.D.

Description: Crystal Structure of Broadly Neutralizing HIV-1 Fusion Peptide-Targeting Antibody VRC34.01 Fab
[[Category: Unreleased Structures]]
[[Category: Kwong, P.D]]
[[Category: Zhou, T]]
[[Category: Xu, K]]
[[Category: Liu, K]]