4xvs - Revision history

OCA at 07:50, 27 September 2023

2023-09-27T07:50:35Z

←Older revision		Revision as of 07:50, 27 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xvs]] is a 3 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=4XVS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XVS FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xvs]] is a 3 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=4XVS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XVS FirstGlance]. <br>
-	</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></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]] 1.9Å</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></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=4xvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xvs OCA], [https://pdbe.org/4xvs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xvs RCSB], [https://www.ebi.ac.uk/pdbsum/4xvs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xvs 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=4xvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xvs OCA], [https://pdbe.org/4xvs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xvs RCSB], [https://www.ebi.ac.uk/pdbsum/4xvs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xvs ProSAT]</span></td></tr>
	</table>		</table>

OCA at 17:54, 26 April 2023

2023-04-26T17:54:29Z

←Older revision		Revision as of 17:54, 26 April 2023
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	<StructureSection load='4xvs' size='340' side='right'caption='[[4xvs]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4xvs' size='340' side='right'caption='[[4xvs]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xvs]] is a 3 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=4XVS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XVS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xvs]] is a 3 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=4XVS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XVS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xvt\|4xvt]]~~</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=4xvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xvs OCA], [https://pdbe.org/4xvs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xvs RCSB], [https://www.ebi.ac.uk/pdbsum/4xvs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xvs 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=4xvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xvs OCA], [~~http~~://pdbe.org/4xvs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xvs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xvs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xvs ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/H9DP89_9HIV1 H9DP89_9HIV1] Envelope glycoprotein gp160: Oligomerizes in the host endoplasmic reticulum into predominantly trimers. In a second time, gp160 transits in the host Golgi, where glycosylation is completed. The precursor is then proteolytically cleaved in the trans-Golgi and thereby activated by cellular furin or furin-like proteases to produce gp120 and gp41.[HAMAP-Rule:MF_04083] Surface protein gp120: Attaches the virus to the host lymphoid cell by binding to the primary receptor CD4. This interaction induces a structural rearrangement creating a high affinity binding site for a chemokine coreceptor like CXCR4 and/or CCR5. Acts as a ligand for CD209/DC-SIGN and CLEC4M/DC-SIGNR, which are respectively found on dendritic cells (DCs), and on endothelial cells of liver sinusoids and lymph node sinuses. These interactions allow capture of viral particles at mucosal surfaces by these cells and subsequent transmission to permissive cells. HIV subverts the migration properties of dendritic cells to gain access to CD4+ T-cells in lymph nodes. Virus transmission to permissive T-cells occurs either in trans (without DCs infection, through viral capture and transmission), or in cis (following DCs productive infection, through the usual CD4-gp120 interaction), thereby inducing a robust infection. In trans infection, bound virions remain infectious over days and it is proposed that they are not degraded, but protected in non-lysosomal acidic organelles within the DCs close to the cell membrane thus contributing to the viral infectious potential during DCs' migration from the periphery to the lymphoid tissues. On arrival at lymphoid tissues, intact virions recycle back to DCs' cell surface allowing virus transmission to CD4+ T-cells.[HAMAP-Rule:MF_04083] Transmembrane protein gp41: Acts as a class I viral fusion protein. Under the current model, the protein has at least 3 conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During fusion of viral and target intracellular membranes, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes. Complete fusion occurs in host cell endosomes and is dynamin-dependent, however some lipid transfer might occur at the plasma membrane. The virus undergoes clathrin-dependent internalization long before endosomal fusion, thus minimizing the surface exposure of conserved viral epitopes during fusion and reducing the efficacy of inhibitors targeting these epitopes. Membranes fusion leads to delivery of the nucleocapsid into the cytoplasm.[HAMAP-Rule:MF_04083]
	<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==
-	*[[Gp120\|Gp120]]	+	*[[Gp120 3D structures\|Gp120 3D structures]]
	== 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: Joyce~~, M G~~]]	+	[[Category: Joyce MG]]
-	[[Category: Kwong~~, P D~~]]	+	[[Category: Kwong PD]]
-	[[Category: Mascola~~, J R]]~~	+	[[Category: Mascola JR]]
-	~~[[Category: Hiv-1 antibodyomics neutralizing antibody germline binding]]~~	+
-	~~[[Category: Viral protein-immune system complex~~]]	+

OCA at 23:24, 5 June 2019

2019-06-05T23:24:24Z

←Older revision		Revision as of 23:24, 5 June 2019
Line 1:		Line 1:

	==Crystal structure of HIV-1 donor 45 d45-01dG5 coreE gp120 with antibody 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995)==		==Crystal structure of HIV-1 donor 45 d45-01dG5 coreE gp120 with antibody 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995)==
-	<StructureSection load='4xvs' size='340' side='right' caption='[[4xvs]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='4xvs' size='340' side='right'caption='[[4xvs]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xvs]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XVS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XVS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xvs]] is a 3 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=4XVS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XVS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xvt\|4xvt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xvt\|4xvt]]</td></tr>
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 4xvs" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4xvs" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Gp120\|Gp120]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Joyce, M G]]		[[Category: Joyce, M G]]
	[[Category: Kwong, P D]]		[[Category: Kwong, P D]]

OCA at 07:50, 27 July 2016

2016-07-27T07:50:20Z

←Older revision		Revision as of 07:50, 27 July 2016
Line 1:		Line 1:
		+
	==Crystal structure of HIV-1 donor 45 d45-01dG5 coreE gp120 with antibody 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995)==		==Crystal structure of HIV-1 donor 45 d45-01dG5 coreE gp120 with antibody 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995)==
	<StructureSection load='4xvs' size='340' side='right' caption='[[4xvs]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4xvs' size='340' side='right' caption='[[4xvs]], [[Resolution\|resolution]] 1.90Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xvt\|4xvt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xvt\|4xvt]]</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=4xvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xvs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xvs RCSB], [http://www.ebi.ac.uk/pdbsum/4xvs PDBsum]</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=4xvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xvs OCA], [http://pdbe.org/4xvs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xvs RCSB], [http://www.ebi.ac.uk/pdbsum/4xvs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xvs ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4xvs" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:47, 6 May 2015

2015-05-06T12:47:39Z

←Older revision		Revision as of 12:47, 6 May 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of HIV-1 donor 45 d45-01dG5 coreE gp120 with antibody 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995)==
		+	<StructureSection load='4xvs' size='340' side='right' caption='[[4xvs]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xvs]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XVS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XVS FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xvt\|4xvt]]</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=4xvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xvs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xvs RCSB], [http://www.ebi.ac.uk/pdbsum/4xvs PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	HIV-1-neutralizing antibodies develop in most HIV-1-infected individuals, although highly effective antibodies are generally observed only after years of chronic infection. Here, we characterize the rate of maturation and extent of diversity for the lineage that produced the broadly neutralizing antibody VRC01 through longitudinal sampling of peripheral B cell transcripts over 15 years and co-crystal structures of lineage members. Next-generation sequencing identified VRC01-lineage transcripts, which encompassed diverse antibodies organized into distinct phylogenetic clades. Prevalent clades maintained characteristic features of antigen recognition, though each evolved binding loops and disulfides that formed distinct recognition surfaces. Over the course of the study period, VRC01-lineage clades showed continuous evolution, with rates of approximately 2 substitutions per 100 nucleotides per year, comparable to that of HIV-1 evolution. This high rate of antibody evolution provides a mechanism by which antibody lineages can achieve extraordinary diversity and, over years of chronic infection, develop effective HIV-1 neutralization.

-	~~The entry 4xvs is ON HOLD until Paper Publication~~	+	Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection.,Wu X, Zhang Z, Schramm CA, Joyce MG, Do Kwon Y, Zhou T, Sheng Z, Zhang B, O'Dell S, McKee K, Georgiev IS, Chuang GY, Longo NS, Lynch RM, Saunders KO, Soto C, Srivatsan S, Yang Y, Bailer RT, Louder MK, Mullikin JC, Connors M, Kwong PD, Mascola JR, Shapiro L Cell. 2015 Apr 8. pii: S0092-8674(15)00257-3. doi: 10.1016/j.cell.2015.03.004. PMID:25865483<ref>PMID:25865483</ref>

-	~~Authors: Joyce~~, M.G.~~, Mascola, J.R., Kwong, P.D~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description:~~	+	== References ==
-	~~[[Category: Unreleased Structures]]~~	+	<references/>
-	[[Category: Joyce, M.G]]	+	__TOC__
-	[[Category: Kwong, P.D]]	+	</StructureSection>
-	[[Category: Mascola, J.R]]	+	[[Category: Joyce, M G]]
		+	[[Category: Kwong, P D]]
		+	[[Category: Mascola, J R]]
		+	[[Category: Hiv-1 antibodyomics neutralizing antibody germline binding]]
		+	[[Category: Viral protein-immune system complex]]

OCA at 11:54, 26 March 2015

2015-03-26T11:54:57Z

←Older revision		Revision as of 11:54, 26 March 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xvs is ON HOLD	+	The entry 4xvs is ON HOLD until Paper Publication

	Authors: Joyce, M.G., Mascola, J.R., Kwong, P.D.		Authors: Joyce, M.G., Mascola, J.R., Kwong, P.D.

OCA at 10:45, 12 February 2015

2015-02-12T10:45:49Z

←Older revision		Revision as of 10:45, 12 February 2015
Line 3:		Line 3:
	The entry 4xvs is ON HOLD		The entry 4xvs is ON HOLD

-	Authors: ~~joyce~~, m.g., ~~mascola~~, j.r., ~~kwong~~, p.d.	+	Authors: Joyce, M.G., Mascola, J.R., Kwong, P.D.

	Description:		Description:

OCA: Protected "4xvs" [edit=sysop:move=sysop]

2015-02-07T14:53:08Z

Protected "4xvs" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:53, 7 February 2015

OCA: New page: '''Unreleased structure''' The entry 4xvs is ON HOLD Authors: joyce, m.g., mascola, j.r., kwong, p.d. Description: Category: Unreleased Structures Category: Joyce, M.G [[Categ...

2015-02-07T14:53:07Z

New page: '''Unreleased structure''' The entry 4xvs is ON HOLD Authors: joyce, m.g., mascola, j.r., kwong, p.d. Description: Category: Unreleased Structures Category: Joyce, M.G [[Categ...

New page

'''Unreleased structure'''

The entry 4xvs is ON HOLD

Authors: joyce, m.g., mascola, j.r., kwong, p.d.

Description:
[[Category: Unreleased Structures]]
[[Category: Joyce, M.G]]
[[Category: Kwong, P.D]]
[[Category: Mascola, J.R]]