6wit - Revision history

OCA at 14:25, 18 October 2023

2023-10-18T14:25:55Z

← Older revision		Revision as of 14:25, 18 October 2023
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	====		==Crystal structure of NHP D15.SD7 Fab in complex with 16055 V1V2 1FD6 scaffold==
	<StructureSection load='6wit' size='340' side='right'caption='[[6wit]]' scene=''>		<StructureSection load='6wit' size='340' side='right'caption='[[6wit]], [[Resolution\|resolution]] 2.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>		<table><tr><td colspan='2'>[[6wit]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Macaca_mulatta Macaca mulatta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WIT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WIT FirstGlance]. <br>
	</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=6wit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wit OCA], [https://pdbe.org/6wit PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wit RCSB], [https://www.ebi.ac.uk/pdbsum/6wit PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wit ProSAT]</span></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]] 2.79Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=6wit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wit OCA], [https://pdbe.org/6wit PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wit RCSB], [https://www.ebi.ac.uk/pdbsum/6wit PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wit ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Understanding the molecular mechanisms by which antibodies target and neutralize the HIV-1 envelope glycoprotein (Env) is critical in guiding immunogen design and vaccine development aimed at eliciting cross-reactive neutralizing antibodies (NAbs). Here, we analyzed monoclonal antibodies (mAbs) isolated from non-human primates (NHPs) immunized with variants of a native flexibly linked (NFL) HIV-1 Env stabilized trimer derived from the tier 2 clade C 16055 strain. The antibodies displayed neutralizing activity against the autologous virus with potencies ranging from 0.005 to 3.68 mug/ml (IC50). Structural characterization using negative-stain EM and X-ray crystallography identified the variable region 2 (V2) of the 16055 NFL trimer to be the common epitope for these antibodies. The crystal structures revealed that the V2 segment adopts a beta-hairpin motif identical to that observed in the 16055 NFL crystal structure. These results depict how vaccine-induced antibodies derived from different clonal lineages penetrate through the glycan shield to recognize a hypervariable region within V2 (residues 184-186) that is unique to the 16055 strain. They also provide potential explanations for the potent autologous neutralization of these antibodies, confirming the immunodominance of this site and revealing that multiple angles of approach are permissible for affinity/avidity that results in potent neutralizing capacity. The structural analysis reveals that the most negatively charged paratope correlated with the potency of the mAbs. The atomic level information is of interest to both define the means of autologous neutralization elicited by different tier 2-based immunogens and facilitate trimer redesign to better target more conserved regions of V2 to potentially elicit cross-neutralizing HIV-1 antibodies.

			Structurally related but genetically unrelated antibody lineages converge on an immunodominant HIV-1 Env neutralizing determinant following trimer immunization.,Aljedani SS, Liban TJ, Tran K, Phad G, Singh S, Dubrovskaya V, Pushparaj P, Martinez-Murillo P, Rodarte J, Mileant A, Mangala Prasad V, Kinzelman R, O'Dell S, Mascola JR, Lee KK, Karlsson Hedestam GB, Wyatt RT, Pancera M PLoS Pathog. 2021 Sep 24;17(9):e1009543. doi: 10.1371/journal.ppat.1009543. , eCollection 2021 Sep. PMID:34559844<ref>PMID:34559844</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6wit" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Z-disk~~]]		[[Category: Macaca mulatta]]
			[[Category: Aljedani S]]
			[[Category: Liban T]]
			[[Category: Pancera M]]
			[[Category: Rodarte J]]

OCA at 06:42, 14 April 2021

2021-04-14T06:42:51Z

← Older revision		Revision as of 06:42, 14 April 2021
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	~~'''Unreleased structure'''~~

	~~The entry~~ 6wit ~~is ON HOLD until Paper Publication~~		====
			<StructureSection load='6wit' size='340' side='right'caption='[[6wit]]' scene=''>
	~~Authors~~: ~~Liban, T~~.~~, Aljedani, S~~.~~, Rodarte, J~~.~~, Pancera, M~~.		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
	~~Description~~: ~~Crystal structure of NHP D15~~.~~SD7 Fab in complex with 16055 V1V2 1FD6 scaffold~~		</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=6wit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wit OCA], [https://pdbe.org/6wit PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wit RCSB], [https://www.ebi.ac.uk/pdbsum/6wit PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wit ProSAT]</span></td></tr>
	[[~~Category~~: ~~Unreleased Structures~~]]		</table>
	[[~~Category~~: ~~Pancera~~, ~~M]]~~		__TOC__
	[~~[Category~~: ~~Aljedani, S]~~]		</StructureSection>
	[[Category: ~~Rodarte, J~~]]		[[Category: Large Structures]]
	[[Category: ~~Liban, T~~]]		[[Category: Z-disk]]

OCA at 09:11, 31 March 2021

2021-03-31T09:11:29Z

← Older revision		Revision as of 09:11, 31 March 2021
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	Authors: Liban, T., Aljedani, S., Rodarte, J., Pancera, M.		Authors: Liban, T., Aljedani, S., Rodarte, J., Pancera, M.

	Description: ~~Structure~~ of NHP ~~GN1-~~SD7 Fab in complex with 16055 V1V2 1FD6 scaffold		Description: Crystal structure of NHP D15.SD7 Fab in complex with 16055 V1V2 1FD6 scaffold
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
			[[Category: Pancera, M]]
	[[Category: Aljedani, S]]		[[Category: Aljedani, S]]
			[[Category: Rodarte, J]]
	[[Category: Liban, T]]		[[Category: Liban, T]]
	~~[[Category: Pancera, M]]~~
	~~[[Category: Rodarte, J]]~~

OCA at 04:50, 10 June 2020

2020-06-10T04:50:20Z

← Older revision		Revision as of 04:50, 10 June 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6wit is ON HOLD		The entry 6wit is ON HOLD until Paper Publication

	Authors: Liban, T., Aljedani, S., Rodarte, J., Pancera, M.		Authors: Liban, T., Aljedani, S., Rodarte, J., Pancera, M.

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

2020-04-22T04:15:46Z

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

← Older revision	Revision as of 04:15, 22 April 2020
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6wit is ON HOLD Authors: Liban, T., Aljedani, S., Rodarte, J., Pancera, M. Description: Structure of NHP GN1-SD7 Fab in complex with 16055 V1V2 1FD...

2020-04-22T04:15:44Z

New page: '''Unreleased structure''' The entry 6wit is ON HOLD Authors: Liban, T., Aljedani, S., Rodarte, J., Pancera, M. Description: Structure of NHP GN1-SD7 Fab in complex with 16055 V1V2 1FD...

New page

'''Unreleased structure'''

The entry 6wit is ON HOLD

Authors: Liban, T., Aljedani, S., Rodarte, J., Pancera, M.

Description: Structure of NHP GN1-SD7 Fab in complex with 16055 V1V2 1FD6 scaffold
[[Category: Unreleased Structures]]
[[Category: Aljedani, S]]
[[Category: Liban, T]]
[[Category: Pancera, M]]
[[Category: Rodarte, J]]