OCA at 15:27, 18 October 2023

OCA — Wed, 18 Oct 2023 15:27:20 GMT

←Older revision		Revision as of 15:27, 18 October 2023
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-	====	+	==Crystal structure of M4H2K1 Fab bound to HIV-1 BG505 gp120 core and to 17b Fab==
-	<StructureSection load='7klc' size='340' side='right'caption='[[7klc]]' scene=''>	+	<StructureSection load='7klc' size='340' side='right'caption='[[7klc]], [[Resolution\|resolution]] 4.30Å' 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'>[[7klc]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens], [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KLC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KLC 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=7klc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7klc OCA], [https://pdbe.org/7klc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7klc RCSB], [https://www.ebi.ac.uk/pdbsum/7klc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7klc 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]] 4.3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</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'>[https://proteopedia.org/fgij/fg.htm?mol=7klc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7klc OCA], [https://pdbe.org/7klc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7klc RCSB], [https://www.ebi.ac.uk/pdbsum/7klc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7klc ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q2N0S5_9HIV1 Q2N0S5_9HIV1] The envelope glyprotein gp160 precursor down-modulates cell surface CD4 antigen by interacting with it in the endoplasmic reticulum and blocking its transport to the cell surface.[RuleBase:RU004292][SAAS:SAAS00139820] The gp120-gp41 heterodimer allows rapid transcytosis of the virus through CD4 negative cells such as simple epithelial monolayers of the intestinal, rectal and endocervical epithelial barriers. Both gp120 and gp41 specifically recognize glycosphingolipids galactosyl-ceramide (GalCer) or 3' sulfo-galactosyl-ceramide (GalS) present in the lipid rafts structures of epithelial cells. Binding to these alternative receptors allows the rapid transcytosis of the virus through the epithelial cells. This transcytotic vesicle-mediated transport of virions from the apical side to the basolateral side of the epithelial cells does not involve infection of the cells themselves.[SAAS:SAAS00140087]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The immunogenicity of gp41-stabilized HIV-1 BG505 envelope (Env) trimers and nanoparticles (NPs) was recently assessed in mice and rabbits. Here, we combined Env-specific B-cell sorting and repertoire sequencing to identify neutralizing antibodies (NAbs) from immunized animals. A panel of mouse NAbs was isolated from mice immunized with a 60-meric I3-01 NP presenting 20 stabilized trimers. Three mouse NAbs potently neutralized BG505.T332N by recognizing a glycan epitope centered in the C3/V4 region on BG505 Env, as revealed by electron microscopy (EM), X-ray crystallography, and epitope mapping. A set of rabbit NAbs was isolated from rabbits immunized with a soluble trimer and a 24-meric ferritin NP presenting 8 trimers. Neutralization assays against BG505.T332N variants confirmed that potent rabbit NAbs targeted previously described glycan holes on BG505 Env and accounted for a significant portion of the autologous NAb response in both the trimer and ferritin NP groups. Last, we examined NAb responses that were induced by non-BG505 Env immunogens. We determined a 3.4-A-resolution crystal structure for the clade C transmitted/founder (T/F) Du172.17 Env with a redesigned heptad repeat 1 (HR1) bend in gp41. This clade C Env, in a soluble trimer form and in a multivalent form with 8 trimers attached to ferritin NP, and the gp41-stabilized clade A Q482-d12 Env trimer elicited distinct NAb responses in rabbits, with notable differences in neutralization breadth. Although eliciting a broad NAb response remains a major challenge, our study provides valuable information on an HIV-1 vaccine design strategy that combines gp41 stabilization and NP display. IMPORTANCE Self-assembling protein nanoparticles (NPs) presenting BG505 envelope (Env) trimers can elicit tier 2 HIV-1-neutralizing antibody (NAb) responses more effectively than soluble trimers. In the present study, monoclonal NAbs were isolated from previously immunized mice and rabbits for structural and functional analyses, which revealed that potent mouse NAbs recognize the C3/V4 region and small NP-elicited rabbit NAbs primarily target known glycan holes on BG505 Env. This study validates the gp41 stabilization strategy for HIV-1 Env vaccine design and highlights the challenge in eliciting a broad NAb response.
		+
		+	Neutralizing Antibodies Induced by First-Generation gp41-Stabilized HIV-1 Envelope Trimers and Nanoparticles.,Kumar S, Lin X, Ngo T, Shapero B, Sou C, Allen JD, Copps J, Zhang L, Ozorowski G, He L, Crispin M, Ward AB, Wilson IA, Zhu J mBio. 2021 Jun 29;12(3):e0042921. doi: 10.1128/mBio.00429-21. Epub 2021 Jun 22. PMID:34156262<ref>PMID:34156262</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7klc" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[Gp120 3D structures\|Gp120 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Human immunodeficiency virus 1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Mus musculus]]
		+	[[Category: Kumar S]]
		+	[[Category: Wilson IA]]

OCA at 09:57, 7 July 2021

OCA — Wed, 07 Jul 2021 09:57:19 GMT

←Older revision		Revision as of 09:57, 7 July 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7klc ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7klc' size='340' side='right'caption='[[7klc]]' scene=''>
-	~~Authors~~: ~~Kumar, S~~.~~, Wilson, I~~.A.	+	== 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 M4H2K1 Fab bound to HIV~~-~~1 BG505 gp120 core and to 17b Fab~~	+	</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=7klc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7klc OCA], [https://pdbe.org/7klc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7klc RCSB], [https://www.ebi.ac.uk/pdbsum/7klc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7klc ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: ~~Kumar, S~~]]	+	__TOC__
-	[[Category: ~~Wilson, I.A~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 13:34, 17 June 2021

OCA — Thu, 17 Jun 2021 13:34:57 GMT

←Older revision		Revision as of 13:34, 17 June 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7klc is ON HOLD	+	The entry 7klc is ON HOLD until Paper Publication

-	Authors:	+	Authors: Kumar, S., Wilson, I.A.

-	Description:	+	Description: Crystal structure of M4H2K1 Fab bound to HIV-1 BG505 gp120 core and to 17b Fab
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Kumar, S]]
		+	[[Category: Wilson, I.A]]

OCA at 13:26, 2 June 2021

OCA — Wed, 02 Jun 2021 13:26:47 GMT

←Older revision		Revision as of 13:26, 2 June 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7klc is ON HOLD ~~until Paper Publication~~	+	The entry 7klc is ON HOLD

	Authors:		Authors:

OCA at 09:12, 10 February 2021

OCA — Wed, 10 Feb 2021 09:12:23 GMT

←Older revision		Revision as of 09:12, 10 February 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7klc is ON HOLD	+	The entry 7klc is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7klc" [edit=sysop:move=sysop]

OCA — Wed, 04 Nov 2020 05:44:41 GMT

Protected "7klc" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:44, 4 November 2020

OCA: New page: '''Unreleased structure''' The entry 7klc is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 04 Nov 2020 05:44:40 GMT

New page: '''Unreleased structure''' The entry 7klc is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7klc is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]