8e1p - Revision history

OCA at 10:16, 25 October 2023

2023-10-25T10:16:48Z

←Older revision		Revision as of 10:16, 25 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8e1p]] is a 18 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=8E1P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8E1P FirstGlance]. <br>		<table><tr><td colspan='2'>[[8e1p]] is a 18 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=8E1P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8E1P FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.82Å</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=8e1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8e1p OCA], [https://pdbe.org/8e1p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8e1p RCSB], [https://www.ebi.ac.uk/pdbsum/8e1p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8e1p ProSAT]</span></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=8e1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8e1p OCA], [https://pdbe.org/8e1p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8e1p RCSB], [https://www.ebi.ac.uk/pdbsum/8e1p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8e1p ProSAT]</span></td></tr>
	</table>		</table>

OCA at 09:37, 21 June 2023

2023-06-21T09:37:51Z

←Older revision		Revision as of 09:37, 21 June 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 8e1p is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of BG505 SOSIP.v4.1-GT1.2 trimer in complex with gl-PGV20 and PGT124 Fabs==
		+	<StructureSection load='8e1p' size='340' side='right'caption='[[8e1p]], [[Resolution\|resolution]] 3.82Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8e1p]] is a 18 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=8E1P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8E1P FirstGlance]. <br>
		+	</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=8e1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8e1p OCA], [https://pdbe.org/8e1p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8e1p RCSB], [https://www.ebi.ac.uk/pdbsum/8e1p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8e1p ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q2N0S6_9HIV1 Q2N0S6_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 (By similarity).[RuleBase:RU004292][SAAS:SAAS000328_004_020447] 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 (By similarity).[SAAS:SAAS000328_004_240990]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Targeting germline (gl-) precursors of broadly neutralizing antibodies (bNAbs) is acknowledged as an important strategy for HIV-1 vaccines. The VRC01-class of bNAbs is attractive because of its distinct genetic signature. However, VRC01-class bNAbs often require extensive somatic hypermutation, including rare insertions and deletions. We describe a BG505 SOSIP trimer, termed GT1.2, to optimize binding to gl-CH31, the unmutated common precursor of the CH30-34 bNAb lineage that acquired a large CDRH1 insertion. The GT1.2 trimer activates gl-CH31 naive B cells in knock-in mice, and B cell responses could be matured by selected boosting immunogens to generate cross-reactive Ab responses. Next-generation B cell sequencing reveals selection for VRC01-class mutations, including insertions in CDRH1 and FWR3 at positions identical to VRC01-class bNAbs, as well as CDRL1 deletions and/or glycine substitutions to accommodate the N276 glycan. These results provide proof of concept for vaccine-induced affinity maturation of B cell lineages that require rare insertions and deletions.

-	~~Authors: Sarkar~~, A., Kumar, S., Wilson, I.A.	+	Germline-targeting HIV-1 Env vaccination induces VRC01-class antibodies with rare insertions.,Caniels TG, Medina-Ramirez M, Zhang J, Sarkar A, Kumar S, LaBranche A, Derking R, Allen JD, Snitselaar JL, Capella-Pujol J, Sanchez IDM, Yasmeen A, Diaz M, Aldon Y, Bijl TPL, Venkatayogi S, Martin Beem JS, Newman A, Jiang C, Lee WH, Pater M, Burger JA, van Breemen MJ, de Taeye SW, Rantalainen K, LaBranche C, Saunders KO, Montefiori D, Ozorowski G, Ward AB, Crispin M, Moore JP, Klasse PJ, Haynes BF, Wilson IA, Wiehe K, Verkoczy L, Sanders RW Cell Rep Med. 2023 Apr 18;4(4):101003. doi: 10.1016/j.xcrm.2023.101003. Epub 2023 , Apr 11. PMID:37044090<ref>PMID:37044090</ref>

-	~~Description: Crystal structure~~ of ~~BG505 SOSIP~~.v4.~~1-GT1~~.~~2 trimer in complex with gl~~-~~PGV20 and PGT124 Fabs~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Kumar, S]]	+	<div class="pdbe-citations 8e1p" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Wilson, I.~~A]]	+	== References ==
-	[[Category: ~~Sarkar, A~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Human immunodeficiency virus 1]]
		+	[[Category: Large Structures]]
		+	[[Category: Kumar S]]
		+	[[Category: Sarkar A]]
		+	[[Category: Wilson IA]]

OCA at 05:45, 11 January 2023

2023-01-11T05:45:45Z

←Older revision		Revision as of 05:45, 11 January 2023
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8e1p is ON HOLD	+	The entry 8e1p is ON HOLD until Paper Publication

	Authors: Sarkar, A., Kumar, S., Wilson, I.A.		Authors: Sarkar, A., Kumar, S., Wilson, I.A.
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	Description: Crystal structure of BG505 SOSIP.v4.1-GT1.2 trimer in complex with gl-PGV20 and PGT124 Fabs		Description: Crystal structure of BG505 SOSIP.v4.1-GT1.2 trimer in complex with gl-PGV20 and PGT124 Fabs
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Wilson, I.A]]
	[[Category: Kumar, S]]		[[Category: Kumar, S]]
		+	[[Category: Wilson, I.A]]
	[[Category: Sarkar, A]]		[[Category: Sarkar, A]]

OCA: Protected "8e1p" [edit=sysop:move=sysop]

2022-08-18T04:15:27Z

Protected "8e1p" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:15, 18 August 2022

OCA: New page: '''Unreleased structure''' The entry 8e1p is ON HOLD Authors: Sarkar, A., Kumar, S., Wilson, I.A. Description: Crystal structure of BG505 SOSIP.v4.1-GT1.2 trimer in complex with gl-PGV...

2022-08-18T04:15:25Z

New page: '''Unreleased structure''' The entry 8e1p is ON HOLD Authors: Sarkar, A., Kumar, S., Wilson, I.A. Description: Crystal structure of BG505 SOSIP.v4.1-GT1.2 trimer in complex with gl-PGV...

New page

'''Unreleased structure'''

The entry 8e1p is ON HOLD

Authors: Sarkar, A., Kumar, S., Wilson, I.A.

Description: Crystal structure of BG505 SOSIP.v4.1-GT1.2 trimer in complex with gl-PGV20 and PGT124 Fabs
[[Category: Unreleased Structures]]
[[Category: Wilson, I.A]]
[[Category: Kumar, S]]
[[Category: Sarkar, A]]