5te7 - Revision history

OCA at 12:58, 4 October 2023

OCA — Wed, 04 Oct 2023 12:58:34 GMT

←Older revision		Revision as of 12:58, 4 October 2023
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	<StructureSection load='5te7' size='340' side='right'caption='[[5te7]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='5te7' size='340' side='right'caption='[[5te7]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5te7]] 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=5TE7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5TE7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5te7]] 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=5TE7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TE7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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]] 2.15Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5te4\|5te4]], [[5te6\|5te6]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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~~://proteopedia.org/fgij/fg.htm?mol=5te7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5te7 OCA], [~~http~~://pdbe.org/5te7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5te7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5te7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5te7 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=5te7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5te7 OCA], [https://pdbe.org/5te7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5te7 RCSB], [https://www.ebi.ac.uk/pdbsum/5te7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5te7 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q202J8_9HIV1 Q202J8_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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	__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: Zhou, T]]	+	[[Category: Zhou T]]
-	~~[[Category: Cd4-binding site]]~~	+
-	~~[[Category: Gp120]]~~	+
-	~~[[Category: Hiv-1]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: N6]]~~	+
-	~~[[Category: Vrc01-class antibody~~]]	+

OCA at 11:31, 16 September 2020

OCA — Wed, 16 Sep 2020 11:31:16 GMT

←Older revision		Revision as of 11:31, 16 September 2020
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	==Crystal Structure of Broadly Neutralizing VRC01-class Antibody N6 in Complex with HIV-1 Clade C Strain DU172.17 gp120 Core==		==Crystal Structure of Broadly Neutralizing VRC01-class Antibody N6 in Complex with HIV-1 Clade C Strain DU172.17 gp120 Core==
-	<StructureSection load='5te7' size='340' side='right' caption='[[5te7]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='5te7' size='340' side='right'caption='[[5te7]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5te7]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TE7 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TE7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5te7]] 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=5TE7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5TE7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <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">[[5te4\|5te4]], [[5te6\|5te6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5te4\|5te4]], [[5te6\|5te6]]</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=5te7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5te7 OCA], [http://pdbe.org/5te7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5te7 RCSB], [http://www.ebi.ac.uk/pdbsum/5te7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5te7 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5te7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5te7 OCA], [http://pdbe.org/5te7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5te7 RCSB], [http://www.ebi.ac.uk/pdbsum/5te7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5te7 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5te7" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5te7" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Gp120 3D structures\|Gp120 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Kwong, P D]]		[[Category: Kwong, P D]]
	[[Category: Zhou, T]]		[[Category: Zhou, T]]

OCA at 03:30, 10 December 2016

OCA — Sat, 10 Dec 2016 03:30:56 GMT

←Older revision		Revision as of 03:30, 10 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5te7 is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of Broadly Neutralizing VRC01-class Antibody N6 in Complex with HIV-1 Clade C Strain DU172.17 gp120 Core==
		+	<StructureSection load='5te7' size='340' side='right' caption='[[5te7]], [[Resolution\|resolution]] 2.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5te7]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TE7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TE7 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <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">[[5te4\|5te4]], [[5te6\|5te6]]</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=5te7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5te7 OCA], [http://pdbe.org/5te7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5te7 RCSB], [http://www.ebi.ac.uk/pdbsum/5te7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5te7 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Detailed studies of the broadly neutralizing antibodies (bNAbs) that underlie the best available examples of the humoral immune response to HIV are providing important information for the development of therapies and prophylaxis for HIV-1 infection. Here, we report a CD4-binding site (CD4bs) antibody, named N6, that potently neutralized 98% of HIV-1 isolates, including 16 of 20 that were resistant to other members of its class. N6 evolved a mode of recognition such that its binding was not impacted by the loss of individual contacts across the immunoglobulin heavy chain. In addition, structural analysis revealed that the orientation of N6 permitted it to avoid steric clashes with glycans, which is a common mechanism of resistance. Thus, an HIV-1-specific bNAb can achieve potent, near-pan neutralization of HIV-1, making it an attractive candidate for use in therapy and prophylaxis.

-	~~Authors:~~ Zhou, T., Kwong, P.D.	+	Identification of a CD4-Binding-Site Antibody to HIV that Evolved Near-Pan Neutralization Breadth.,Huang J, Kang BH, Ishida E, Zhou T, Griesman T, Sheng Z, Wu F, Doria-Rose NA, Zhang B, McKee K, O'Dell S, Chuang GY, Druz A, Georgiev IS, Schramm CA, Zheng A, Joyce MG, Asokan M, Ransier A, Darko S, Migueles SA, Bailer RT, Louder MK, Alam SM, Parks R, Kelsoe G, Von Holle T, Haynes BF, Douek DC, Hirsch V, Seaman MS, Shapiro L, Mascola JR, Kwong PD, Connors M Immunity. 2016 Nov 15;45(5):1108-1121. doi: 10.1016/j.immuni.2016.10.027. PMID:27851912<ref>PMID:27851912</ref>

-	~~Description: Crystal Structure~~ of ~~Broadly Neutralizing VRC01-class Antibody N6 in complex with HIV-1 Clade C strain DU172~~.~~17 core gp120~~	+	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 5te7" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kwong, P D]]
	[[Category: Zhou, T]]		[[Category: Zhou, T]]
		+	[[Category: Cd4-binding site]]
		+	[[Category: Gp120]]
		+	[[Category: Hiv-1]]
		+	[[Category: Immune system]]
		+	[[Category: N6]]
		+	[[Category: Vrc01-class antibody]]

OCA at 15:42, 19 October 2016

OCA — Wed, 19 Oct 2016 15:42:35 GMT

←Older revision		Revision as of 15:42, 19 October 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5te7 is ON HOLD	+	The entry 5te7 is ON HOLD until Paper Publication

	Authors: Zhou, T., Kwong, P.D.		Authors: Zhou, T., Kwong, P.D.

OCA at 19:58, 5 October 2016

OCA — Wed, 05 Oct 2016 19:58:25 GMT

←Older revision		Revision as of 19:58, 5 October 2016
Line 3:		Line 3:
	The entry 5te7 is ON HOLD		The entry 5te7 is ON HOLD

-	Authors: Zhou, T, Kwong, PD	+	Authors: Zhou, T., Kwong, P.D.

	Description: Crystal Structure of Broadly Neutralizing VRC01-class Antibody N6 in complex with HIV-1 Clade C strain DU172.17 core gp120		Description: Crystal Structure of Broadly Neutralizing VRC01-class Antibody N6 in complex with HIV-1 Clade C strain DU172.17 core gp120
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Zhou, T~~, Kwong, Pd~~]]	+	[[Category: Kwong, P.D]]
		+	[[Category: Zhou, T]]

OCA: Protected "5te7" [edit=sysop:move=sysop]

OCA — Mon, 03 Oct 2016 15:32:31 GMT

Protected "5te7" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:32, 3 October 2016

OCA: New page: '''Unreleased structure''' The entry 5te7 is ON HOLD Authors: Zhou, T, Kwong, PD Description: Crystal Structure of Broadly Neutralizing VRC01-class Antibody N6 in complex with HIV-1 Cl...

OCA — Mon, 03 Oct 2016 15:32:29 GMT

New page: '''Unreleased structure''' The entry 5te7 is ON HOLD Authors: Zhou, T, Kwong, PD Description: Crystal Structure of Broadly Neutralizing VRC01-class Antibody N6 in complex with HIV-1 Cl...

New page

'''Unreleased structure'''

The entry 5te7 is ON HOLD

Authors: Zhou, T, Kwong, PD

Description: Crystal Structure of Broadly Neutralizing VRC01-class Antibody N6 in complex with HIV-1 Clade C strain DU172.17 core gp120
[[Category: Unreleased Structures]]
[[Category: Zhou, T, Kwong, Pd]]