5v7j - Revision history

OCA at 13:43, 4 October 2023

2023-10-04T13:43:22Z

←Older revision		Revision as of 13:43, 4 October 2023
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	<StructureSection load='5v7j' size='340' side='right'caption='[[5v7j]], [[Resolution\|resolution]] 2.91Å' scene=''>		<StructureSection load='5v7j' size='340' side='right'caption='[[5v7j]], [[Resolution\|resolution]] 2.91Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v7j]] is a 6 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=5V7J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5V7J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v7j]] is a 6 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=5V7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V7J 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=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]] 2.907Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">env ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])~~</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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5v7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7j OCA], [~~http~~://pdbe.org/5v7j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5v7j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5v7j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7j 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=5v7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7j OCA], [https://pdbe.org/5v7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v7j RCSB], [https://www.ebi.ac.uk/pdbsum/5v7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://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]	+	[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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 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: Human immunodeficiency virus 1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kwong~~, P D~~]]	+	[[Category: Kwong PD]]
-	[[Category: Stewart-Jones~~, G B.E~~]]	+	[[Category: Stewart-Jones GBE]]
-	[[Category: Zhou, T]]	+	[[Category: Zhou T]]
-	~~[[Category: Antibody]]~~	+
-	~~[[Category: Envelope]]~~	+
-	~~[[Category: Hiv-1]]~~	+
-	~~[[Category: Viral protein-immune system complex]]~~	+
-	~~[[Category: Virus~~]]	+

OCA at 17:14, 11 December 2019

2019-12-11T17:14:46Z

←Older revision		Revision as of 17:14, 11 December 2019
Line 1:		Line 1:

	==Crystal Structure at 3.7 A Resolution of Glycosylated HIV-1 Clade A BG505 SOSIP.664 Prefusion Env Trimer with Four Glycans (N197, N276, N362, and N462) removed in Complex with Neutralizing Antibodies 3H+109L and 35O22.==		==Crystal Structure at 3.7 A Resolution of Glycosylated HIV-1 Clade A BG505 SOSIP.664 Prefusion Env Trimer with Four Glycans (N197, N276, N362, and N462) removed in Complex with Neutralizing Antibodies 3H+109L and 35O22.==
-	<StructureSection load='5v7j' size='340' side='right' caption='[[5v7j]], [[Resolution\|resolution]] 2.91Å' scene=''>	+	<StructureSection load='5v7j' size='340' side='right'caption='[[5v7j]], [[Resolution\|resolution]] 2.91Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v7j]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v7j]] is a 6 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=5V7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7J 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=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=MAN:ALPHA-D-MANNOSE'>MAN</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">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=5v7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7j OCA], [http://pdbe.org/5v7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v7j RCSB], [http://www.ebi.ac.uk/pdbsum/5v7j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7j 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=5v7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7j OCA], [http://pdbe.org/5v7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v7j RCSB], [http://www.ebi.ac.uk/pdbsum/5v7j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7j ProSAT]</span></td></tr>
	</table>		</table>
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5v7j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5v7j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Kwong, P D]]		[[Category: Kwong, P D]]
	[[Category: Stewart-Jones, G B.E]]		[[Category: Stewart-Jones, G B.E]]

OCA at 11:07, 24 August 2017

2017-08-24T11:07:33Z

←Older revision		Revision as of 11:07, 24 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5v7j is ~~ON HOLD~~	+	==Crystal Structure at 3.7 A Resolution of Glycosylated HIV-1 Clade A BG505 SOSIP.664 Prefusion Env Trimer with Four Glycans (N197, N276, N362, and N462) removed in Complex with Neutralizing Antibodies 3H+109L and 35O22.==
		+	<StructureSection load='5v7j' size='340' side='right' caption='[[5v7j]], [[Resolution\|resolution]] 2.91Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5v7j]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7J 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=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=5v7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7j OCA], [http://pdbe.org/5v7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v7j RCSB], [http://www.ebi.ac.uk/pdbsum/5v7j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7j ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://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 ==
		+	While the HIV-1-glycan shield is known to shelter Env from the humoral immune response, its quantitative impact on antibody elicitation has been unclear. Here, we use targeted deglycosylation to measure the impact of the glycan shield on elicitation of antibodies against the CD4 supersite. We engineered diverse Env trimers with select glycans removed proximal to the CD4 supersite, characterized their structures and glycosylation, and immunized guinea pigs and rhesus macaques. Immunizations yielded little neutralization against wild-type viruses but potent CD4-supersite neutralization (titers 1: >1,000,000 against four-glycan-deleted autologous viruses with over 90% breadth against four-glycan-deleted heterologous strains exhibiting tier 2 neutralization character). To a first approximation, the immunogenicity of the glycan-shielded protein surface was negligible, with Env-elicited neutralization (ID50) proportional to the exponential of the protein-surface area accessible to antibody. Based on these high titers and exponential relationship, we propose site-selective deglycosylated trimers as priming immunogens to increase the frequency of site-targeting antibodies.

-	~~Authors:~~ Stewart-Jones, G.B~~.E.~~, ~~Zhou~~, T., ~~Kwong~~, P.D.	+	Quantification of the Impact of the HIV-1-Glycan Shield on Antibody Elicitation.,Zhou T, Doria-Rose NA, Cheng C, Stewart-Jones GBE, Chuang GY, Chambers M, Druz A, Geng H, McKee K, Kwon YD, O'Dell S, Sastry M, Schmidt SD, Xu K, Chen L, Chen RE, Louder MK, Pancera M, Wanninger TG, Zhang B, Zheng A, Farney SK, Foulds KE, Georgiev IS, Joyce MG, Lemmin T, Narpala S, Rawi R, Soto C, Todd JP, Shen CH, Tsybovsky Y, Yang Y, Zhao P, Haynes BF, Stamatatos L, Tiemeyer M, Wells L, Scorpio DG, Shapiro L, McDermott AB, Mascola JR, Kwong PD Cell Rep. 2017 Apr 25;19(4):719-732. doi: 10.1016/j.celrep.2017.04.013. PMID:28445724<ref>PMID:28445724</ref>

-	~~Description: Crystal Structure at 3.7 A Resolution~~ of ~~Glycosylated HIV-1 Clade A BG505 SOSIP~~.~~664 Prefusion Env Trimer with Four Glycans (N197, N276, N362, and N462) removed in Complex with Neutralizing Antibodies 3H+109L and 35O22~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Kwong~~, P.D]]	+	<div class="pdbe-citations 5v7j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kwong, P D]]
		+	[[Category: Stewart-Jones, G B.E]]
	[[Category: Zhou, T]]		[[Category: Zhou, T]]
-	[[Category: ~~Stewart~~-~~Jones, G.B.E~~]]	+	[[Category: Antibody]]
		+	[[Category: Envelope]]
		+	[[Category: Hiv-1]]
		+	[[Category: Viral protein-immune system complex]]
		+	[[Category: Virus]]

OCA: Protected "5v7j" [edit=sysop:move=sysop]

2017-04-05T11:41:34Z

Protected "5v7j" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:41, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5v7j is ON HOLD Authors: Stewart-Jones, G.B.E., Zhou, T., Kwong, P.D. Description: Crystal Structure at 3.7 A Resolution of Glycosylated HIV-1 Clad...

2017-04-05T11:41:33Z

New page: '''Unreleased structure''' The entry 5v7j is ON HOLD Authors: Stewart-Jones, G.B.E., Zhou, T., Kwong, P.D. Description: Crystal Structure at 3.7 A Resolution of Glycosylated HIV-1 Clad...

New page

'''Unreleased structure'''

The entry 5v7j is ON HOLD

Authors: Stewart-Jones, G.B.E., Zhou, T., Kwong, P.D.

Description: Crystal Structure at 3.7 A Resolution of Glycosylated HIV-1 Clade A BG505 SOSIP.664 Prefusion Env Trimer with Four Glycans (N197, N276, N362, and N462) removed in Complex with Neutralizing Antibodies 3H+109L and 35O22.
[[Category: Unreleased Structures]]
[[Category: Kwong, P.D]]
[[Category: Zhou, T]]
[[Category: Stewart-Jones, G.B.E]]