6db6 - Revision history

OCA at 10:03, 18 December 2019

2019-12-18T10:03:07Z

←Older revision		Revision as of 10:03, 18 December 2019
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	==Crystal structure of anti-HIV-1 V3 Fab 311-11D in complex with a HIV-1 gp120 V3 peptide from MN strain==		==Crystal structure of anti-HIV-1 V3 Fab 311-11D in complex with a HIV-1 gp120 V3 peptide from MN strain==
-	<StructureSection load='6db6' size='340' side='right' caption='[[6db6]], [[Resolution\|resolution]] 1.98Å' scene=''>	+	<StructureSection load='6db6' size='340' side='right'caption='[[6db6]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6db6]] is a 3 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=6DB6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DB6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6db6]] is a 3 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=6DB6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DB6 FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Chan, K W]]		[[Category: Chan, K W]]
	[[Category: Kong, X P]]		[[Category: Kong, X P]]

OCA at 07:51, 12 September 2018

2018-09-12T07:51:56Z

←Older revision		Revision as of 07:51, 12 September 2018
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	<StructureSection load='6db6' size='340' side='right' caption='[[6db6]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='6db6' size='340' side='right' caption='[[6db6]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6db6]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DB6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DB6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6db6]] is a 3 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=6DB6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DB6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FCA:ALPHA-D-FUCOSE'>FCA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FCA:ALPHA-D-FUCOSE'>FCA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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=6db6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6db6 OCA], [http://pdbe.org/6db6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6db6 RCSB], [http://www.ebi.ac.uk/pdbsum/6db6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6db6 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=6db6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6db6 OCA], [http://pdbe.org/6db6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6db6 RCSB], [http://www.ebi.ac.uk/pdbsum/6db6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6db6 ProSAT]</span></td></tr>
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	</div>		</div>
	<div class="pdbe-citations 6db6" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6db6" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Chan, K W]]		[[Category: Chan, K W]]
	[[Category: Kong, X P]]		[[Category: Kong, X P]]

OCA at 07:36, 25 July 2018

2018-07-25T07:36:15Z

←Older revision		Revision as of 07:36, 25 July 2018
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	<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=6db6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6db6 OCA], [http://pdbe.org/6db6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6db6 RCSB], [http://www.ebi.ac.uk/pdbsum/6db6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6db6 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=6db6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6db6 OCA], [http://pdbe.org/6db6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6db6 RCSB], [http://www.ebi.ac.uk/pdbsum/6db6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6db6 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Elucidating the structural basis of antibody (Ab) gene usage and affinity maturation of vaccine-induced Abs can inform the design of immunogens for inducing desired Ab responses in HIV vaccine development. Analyses of monoclonal Abs (mAbs) encoded by the same immunoglobulin genes in different stages of maturation can help to understand the maturation process. We have analyzed four human anti-V3 mAbs with the same VH1-301 and VL3-1001 gene usage. Two mAbs, TA6 and TA7, were developed from a vaccinee in the HIV vaccine phase I trial DP6-001 with a polyvalent DNA prime - protein boost regimen, and two others, 311-11D and 1334, were developed from HIV-infected patients. The somatic hypermutation (SHM) rates in VH of vaccine-induced mAbs are lower than in chronic HIV infection-induced mAbs, while those in VL are comparable. Crystal structures of the antigen-binding fragments (Fabs) in complex with V3 peptides show that these mAbs bind the V3 epitope with a new cradle-binding mode, and that the V3 beta-hairpin lies along the antigen-binding groove, which consists of residues from both heavy and light chains. Residues conserved from the germline sequences form specific binding pockets accommodating conserved structural elements of the V3 crown hairpin, predetermining the Ab gene selection, while somatically mutated residues create additional hydrogen bonds, electrostatic interactions, and van der Waals contacts, correlating with an increased binding affinity. Our data provide a unique example of germline sequences determining the primordial antigen-binding sites and SHMs correlating with affinity maturation of Abs induced by vaccine and natural HIV infection.IMPORTANCE Understanding the structural basis of gene usage and affinity maturation for anti-HIV-1 antibodies may help vaccine design and development. Antibodies targeting the highly immunogenic third variable loop (V3) of HIV-1 gp120 provide a unique opportunity for detailed structural investigations. By comparing the sequences and structures of four anti-V3 mAbs at different stages of affinity maturation but of the same V gene usage, two induced by vaccination and another two by chronic infection, we provide a fine example of how germline sequence determines the essential elements for epitope recognition and how affinity maturation improves the antibody's recognition of its epitope.
		+
		+	Structural Comparison of Human Anti-HIV-1 gp120 V3 MAbs of the Same Gene Usage Induced by Vaccination and Chronic Infection.,Chan KW, Pan R, Costa M, Gorny MK, Wang S, Lu S, Kong XP J Virol. 2018 Jul 11. pii: JVI.00641-18. doi: 10.1128/JVI.00641-18. PMID:29997214<ref>PMID:29997214</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6db6" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:43, 11 July 2018

2018-07-11T05:43:50Z

←Older revision		Revision as of 05:43, 11 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6db6 is ON HOLD until Paper Publication~~	+	==Crystal structure of anti-HIV-1 V3 Fab 311-11D in complex with a HIV-1 gp120 V3 peptide from MN strain==
-		+	<StructureSection load='6db6' size='340' side='right' caption='[[6db6]], [[Resolution\|resolution]] 1.98Å' scene=''>
-	~~Authors: Chan, K.-W., Kong, X.-P.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6db6]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DB6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DB6 FirstGlance]. <br>
-	~~Description:~~ Crystal structure of anti-HIV-1 V3 Fab 311-11D in complex with a HIV-1 gp120 V3 peptide from MN strain	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FCA:ALPHA-D-FUCOSE'>FCA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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=6db6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6db6 OCA], [http://pdbe.org/6db6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6db6 RCSB], [http://www.ebi.ac.uk/pdbsum/6db6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6db6 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Kong~~, X.-P]]	+	</table>
-	[[Category: Chan, K.-W]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Chan, K W]]
		+	[[Category: Kong, X P]]
		+	[[Category: Gp120]]
		+	[[Category: Hiv-1]]
		+	[[Category: Immune system]]
		+	[[Category: Mab]]
		+	[[Category: V3]]

OCA at 04:03, 16 May 2018

2018-05-16T04:03:36Z

←Older revision		Revision as of 04:03, 16 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6db6 is ON HOLD	+	The entry 6db6 is ON HOLD until Paper Publication

	Authors: Chan, K.-W., Kong, X.-P.		Authors: Chan, K.-W., Kong, X.-P.

-	Description: Crystal structure of anti-HIV-1 V3 Fab 311-11D in complex with a MN V3 peptide	+	Description: Crystal structure of anti-HIV-1 V3 Fab 311-11D in complex with a HIV-1 gp120 V3 peptide from MN strain
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Kong, X.-P]]		[[Category: Kong, X.-P]]
	[[Category: Chan, K.-W]]		[[Category: Chan, K.-W]]

OCA: Protected "6db6" [edit=sysop:move=sysop]

2018-05-09T04:57:25Z

Protected "6db6" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:57, 9 May 2018

OCA: New page: '''Unreleased structure''' The entry 6db6 is ON HOLD Authors: Chan, K.-W., Kong, X.-P. Description: Crystal structure of anti-HIV-1 V3 Fab 311-11D in complex with a MN V3 peptide [[Cat...

2018-05-09T04:57:24Z

New page: '''Unreleased structure''' The entry 6db6 is ON HOLD Authors: Chan, K.-W., Kong, X.-P. Description: Crystal structure of anti-HIV-1 V3 Fab 311-11D in complex with a MN V3 peptide [[Cat...

New page

'''Unreleased structure'''

The entry 6db6 is ON HOLD

Authors: Chan, K.-W., Kong, X.-P.

Description: Crystal structure of anti-HIV-1 V3 Fab 311-11D in complex with a MN V3 peptide
[[Category: Unreleased Structures]]
[[Category: Kong, X.-P]]
[[Category: Chan, K.-W]]