5f96 - Revision history

OCA at 06:42, 19 July 2023

OCA — Wed, 19 Jul 2023 06:42:45 GMT

←Older revision		Revision as of 06:42, 19 July 2023
Line 1:		Line 1:

	==Crystal structure of broadly neutralizing VH1-46 germline-derived CD4-binding site-directed antibody CH235.12 in complex with HIV-1 clade A/E 93TH057 gp120==		==Crystal structure of broadly neutralizing VH1-46 germline-derived CD4-binding site-directed antibody CH235.12 in complex with HIV-1 clade A/E 93TH057 gp120==
-	<StructureSection load='5f96' size='340' side='right' caption='[[5f96]], [[Resolution\|resolution]] 2.24Å' scene=''>	+	<StructureSection load='5f96' size='340' side='right'caption='[[5f96]], [[Resolution\|resolution]] 2.24Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5f96]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~9hiv1 9hiv1~~] and [~~http~~://en.wikipedia.org/wiki/Human ~~Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F96 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5F96 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5f96]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F96 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5F96 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=EPE:4~~-(2~~-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.2407Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[4rx4\|4rx4]], [[4rwy\|4rwy]], [[4yfl\|4yfl]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">HIV-1 Env ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])~~</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=5f96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f96 OCA], [https://pdbe.org/5f96 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5f96 RCSB], [https://www.ebi.ac.uk/pdbsum/5f96 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5f96 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=5f96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f96 OCA], [~~http~~://pdbe.org/5f96 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5f96 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5f96 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5f96 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0M3KKW9_9HIV1 A0A0M3KKW9_9HIV1]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 21:

	==See Also==		==See Also==
-	*[[3D structures of antibody\|3D structures of antibody]]	+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[Gp120 3D structures\|Gp120 3D structures]]
		+	*[[3D structures of human antibody\|3D structures of human antibody]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Kwong, P D~~]]	+	[[Category: Human immunodeficiency virus 1]]
-	[[Category: ~~Zhou, T~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Antibody~~]]	+	[[Category: Kwong PD]]
-	[[Category: ~~Ch235 lineage]]~~	+	[[Category: Zhou T]]
-	~~[[Category: Hiv-1]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Vh1-46 germline~~]]	+

OCA at 09:56, 22 November 2017

OCA — Wed, 22 Nov 2017 09:56:48 GMT

←Older revision		Revision as of 09:56, 22 November 2017
Line 5:		Line 5:
	<table><tr><td colspan='2'>[[5f96]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/9hiv1 9hiv1] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F96 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F96 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5f96]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/9hiv1 9hiv1] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F96 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F96 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rx4\|4rx4]], [[4rwy\|4rwy]], [[4yfl\|4yfl]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HIV-1 Env ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HIV-1 Env ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])</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=5f96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f96 OCA], [http://pdbe.org/5f96 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f96 RCSB], [http://www.ebi.ac.uk/pdbsum/5f96 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5f96 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=5f96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f96 OCA], [http://pdbe.org/5f96 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f96 RCSB], [http://www.ebi.ac.uk/pdbsum/5f96 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5f96 ProSAT]</span></td></tr>

OCA at 13:18, 16 November 2017

OCA — Thu, 16 Nov 2017 13:18:07 GMT

←Older revision		Revision as of 13:18, 16 November 2017
Line 3:		Line 3:
	<StructureSection load='5f96' size='340' side='right' caption='[[5f96]], [[Resolution\|resolution]] 2.24Å' scene=''>		<StructureSection load='5f96' size='340' side='right' caption='[[5f96]], [[Resolution\|resolution]] 2.24Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5f96]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F96 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F96 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5f96]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/9hiv1 9hiv1] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F96 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F96 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=5f96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f96 OCA], [http://pdbe.org/5f96 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f96 RCSB], [http://www.ebi.ac.uk/pdbsum/5f96 PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HIV-1 Env ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])</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=5f96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f96 OCA], [http://pdbe.org/5f96 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f96 RCSB], [http://www.ebi.ac.uk/pdbsum/5f96 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5f96 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5f96" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5f96" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[3D structures of antibody\|3D structures of antibody]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Kwong, P D]]		[[Category: Kwong, P D]]
	[[Category: Zhou, T]]		[[Category: Zhou, T]]

OCA at 18:34, 10 May 2016

OCA — Tue, 10 May 2016 18:34:03 GMT

←Older revision		Revision as of 18:34, 10 May 2016
Line 7:		Line 7:
	<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=5f96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f96 OCA], [http://pdbe.org/5f96 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f96 RCSB], [http://www.ebi.ac.uk/pdbsum/5f96 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=5f96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f96 OCA], [http://pdbe.org/5f96 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f96 RCSB], [http://www.ebi.ac.uk/pdbsum/5f96 PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Antibodies with ontogenies from VH1-2 or VH1-46-germline genes dominate the broadly neutralizing response against the CD4-binding site (CD4bs) on HIV-1. Here, we define with longitudinal sampling from time-of-infection the development of a VH1-46-derived antibody lineage that matured to neutralize 90% of HIV-1 isolates. Structures of lineage antibodies CH235 (week 41 from time-of-infection, 18% breadth), CH235.9 (week 152, 77%), and CH235.12 (week 323, 90%) demonstrated the maturing epitope to focus on the conformationally invariant portion of the CD4bs. Similarities between CH235 lineage and five unrelated CD4bs lineages in epitope focusing, length-of-time to develop breadth, and extraordinary level of somatic hypermutation suggested commonalities in maturation among all CD4bs antibodies. Fortunately, the required CH235-lineage hypermutation appeared substantially guided by the intrinsic mutability of the VH1-46 gene, which closely resembled VH1-2. We integrated our CH235-lineage findings with a second broadly neutralizing lineage and HIV-1 co-evolution to suggest a vaccination strategy for inducing both lineages.
		+
		+	Maturation Pathway from Germline to Broad HIV-1 Neutralizer of a CD4-Mimic Antibody.,Bonsignori M, Zhou T, Sheng Z, Chen L, Gao F, Joyce MG, Ozorowski G, Chuang GY, Schramm CA, Wiehe K, Alam SM, Bradley T, Gladden MA, Hwang KK, Iyengar S, Kumar A, Lu X, Luo K, Mangiapani MC, Parks RJ, Song H, Acharya P, Bailer RT, Cao A, Druz A, Georgiev IS, Kwon YD, Louder MK, Zhang B, Zheng A, Hill BJ, Kong R, Soto C, Mullikin JC, Douek DC, Montefiori DC, Moody MA, Shaw GM, Hahn BH, Kelsoe G, Hraber PT, Korber BT, Boyd SD, Fire AZ, Kepler TB, Shapiro L, Ward AB, Mascola JR, Liao HX, Kwong PD, Haynes BF Cell. 2016 Apr 7;165(2):449-63. doi: 10.1016/j.cell.2016.02.022. Epub 2016 Mar 3. PMID:26949186<ref>PMID:26949186</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5f96" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 03:57, 10 March 2016

OCA — Thu, 10 Mar 2016 03:57:25 GMT

←Older revision		Revision as of 03:57, 10 March 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5f96 is ON HOLD until Paper Publication~~	+	==Crystal structure of broadly neutralizing VH1-46 germline-derived CD4-binding site-directed antibody CH235.12 in complex with HIV-1 clade A/E 93TH057 gp120==
-		+	<StructureSection load='5f96' size='340' side='right' caption='[[5f96]], [[Resolution\|resolution]] 2.24Å' scene=''>
-	~~Authors: Zhou, T., Kwong, P.D.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5f96]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F96 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F96 FirstGlance]. <br>
-	~~Description:~~ Crystal structure of broadly neutralizing VH1-46 germline-derived CD4-binding site-directed antibody CH235.12 in complex with HIV-1 clade A/E 93TH057 gp120	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5f96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f96 OCA], [http://pdbe.org/5f96 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f96 RCSB], [http://www.ebi.ac.uk/pdbsum/5f96 PDBsum]</span></td></tr>
-	[[Category: Kwong, P.D]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kwong, P D]]
	[[Category: Zhou, T]]		[[Category: Zhou, T]]
		+	[[Category: Antibody]]
		+	[[Category: Ch235 lineage]]
		+	[[Category: Hiv-1]]
		+	[[Category: Immune system]]
		+	[[Category: Vh1-46 germline]]

OCA at 18:00, 13 January 2016

OCA — Wed, 13 Jan 2016 18:00:20 GMT

←Older revision		Revision as of 18:00, 13 January 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5f96 is ON HOLD	+	The entry 5f96 is ON HOLD until Paper Publication

	Authors: Zhou, T., Kwong, P.D.		Authors: Zhou, T., Kwong, P.D.

OCA: Protected "5f96" [edit=sysop:move=sysop]

OCA — Wed, 16 Dec 2015 12:45:16 GMT

Protected "5f96" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:45, 16 December 2015

OCA: New page: '''Unreleased structure''' The entry 5f96 is ON HOLD Authors: Zhou, T., Kwong, P.D. Description: Crystal structure of broadly neutralizing VH1-46 germline-derived CD4-binding site-dire...

OCA — Wed, 16 Dec 2015 12:45:15 GMT

New page: '''Unreleased structure''' The entry 5f96 is ON HOLD Authors: Zhou, T., Kwong, P.D. Description: Crystal structure of broadly neutralizing VH1-46 germline-derived CD4-binding site-dire...

New page

'''Unreleased structure'''

The entry 5f96 is ON HOLD

Authors: Zhou, T., Kwong, P.D.

Description: Crystal structure of broadly neutralizing VH1-46 germline-derived CD4-binding site-directed antibody CH235.12 in complex with HIV-1 clade A/E 93TH057 gp120
[[Category: Unreleased Structures]]
[[Category: Kwong, P.D]]
[[Category: Zhou, T]]