5i8c - Revision history

OCA at 08:26, 23 August 2023

OCA — Wed, 23 Aug 2023 08:26:32 GMT

←Older revision		Revision as of 08:26, 23 August 2023
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	<StructureSection load='5i8c' size='340' side='right'caption='[[5i8c]], [[Resolution\|resolution]] 1.54Å' scene=''>		<StructureSection load='5i8c' size='340' side='right'caption='[[5i8c]], [[Resolution\|resolution]] 1.54Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i8c]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human ~~Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I8C OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5I8C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i8c]] 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=5I8C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I8C FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5i8h\|5i8h]], [[5i8e\|5i8e]]</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]] 1.54Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">IGHG1 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=9606 HUMAN])~~</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=5i8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8c OCA], [https://pdbe.org/5i8c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i8c RCSB], [https://www.ebi.ac.uk/pdbsum/5i8c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8c 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=5i8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8c OCA], [~~http~~://pdbe.org/5i8c PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5i8c RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5i8c PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8c ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q2N0S7_9HIV1 Q2N0S7_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: Liu, K]]	+	[[Category: Liu K]]
-	[[Category: Xu, K]]	+	[[Category: Xu K]]
-	[[Category: Zhou, T]]	+	[[Category: Zhou T]]
-	~~[[Category: Antibody]]~~	+
-	~~[[Category: Envelope]]~~	+
-	~~[[Category: Fusion peptide]]~~	+
-	~~[[Category: Hiv-1]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Neutralizing]]~~	+
-	~~[[Category: Trimer~~]]	+

OCA at 16:16, 11 December 2019

OCA — Wed, 11 Dec 2019 16:16:24 GMT

←Older revision		Revision as of 16:16, 11 December 2019
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	==Crystal Structure of HIV-1 Clade A BG505 Fusion Peptide (residue 512-520) in Complex with Broadly Neutralizing Antibody VRC34.01 Fab==		==Crystal Structure of HIV-1 Clade A BG505 Fusion Peptide (residue 512-520) in Complex with Broadly Neutralizing Antibody VRC34.01 Fab==
-	<StructureSection load='5i8c' size='340' side='right' caption='[[5i8c]], [[Resolution\|resolution]] 1.54Å' scene=''>	+	<StructureSection load='5i8c' size='340' side='right'caption='[[5i8c]], [[Resolution\|resolution]] 1.54Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i8c]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I8C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I8C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i8c]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I8C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I8C FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i8h\|5i8h]], [[5i8e\|5i8e]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i8h\|5i8h]], [[5i8e\|5i8e]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IGHG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5i8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8c OCA], [http://pdbe.org/5i8c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i8c RCSB], [http://www.ebi.ac.uk/pdbsum/5i8c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8c 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=5i8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8c OCA], [http://pdbe.org/5i8c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i8c RCSB], [http://www.ebi.ac.uk/pdbsum/5i8c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8c ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Kwong, P D]]		[[Category: Kwong, P D]]
	[[Category: Liu, K]]		[[Category: Liu, K]]

OCA at 04:40, 21 September 2017

OCA — Thu, 21 Sep 2017 04:40:32 GMT

←Older revision		Revision as of 04:40, 21 September 2017
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	<table><tr><td colspan='2'>[[5i8c]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I8C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I8C FirstGlance]. <br>		<table><tr><td colspan='2'>[[5i8c]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I8C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I8C FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i8h\|5i8h]], [[5i8e\|5i8e]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i8h\|5i8h]], [[5i8e\|5i8e]]</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=5i8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8c OCA], [http://pdbe.org/5i8c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i8c RCSB], [http://www.ebi.ac.uk/pdbsum/5i8c 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=5i8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8c OCA], [http://pdbe.org/5i8c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i8c RCSB], [http://www.ebi.ac.uk/pdbsum/5i8c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8c ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:00, 1 June 2016

OCA — Wed, 01 Jun 2016 23:00:16 GMT

←Older revision		Revision as of 23:00, 1 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5i8c is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of HIV-1 Clade A BG505 Fusion Peptide (residue 512-520) in Complex with Broadly Neutralizing Antibody VRC34.01 Fab==
		+	<StructureSection load='5i8c' size='340' side='right' caption='[[5i8c]], [[Resolution\|resolution]] 1.54Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5i8c]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I8C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I8C FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i8h\|5i8h]], [[5i8e\|5i8e]]</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=5i8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8c OCA], [http://pdbe.org/5i8c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i8c RCSB], [http://www.ebi.ac.uk/pdbsum/5i8c PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The HIV-1 fusion peptide, comprising 15 to 20 hydrophobic residues at the N terminus of the Env-gp41 subunit, is a critical component of the virus-cell entry machinery. Here, we report the identification of a neutralizing antibody, N123-VRC34.01, which targets the fusion peptide and blocks viral entry by inhibiting conformational changes in gp120 and gp41 subunits of Env required for entry. Crystal structures of N123-VRC34.01 liganded to the fusion peptide, and to the full Env trimer, revealed an epitope consisting of the N-terminal eight residues of the gp41 fusion peptide and glycan N88 of gp120, and molecular dynamics showed that the N-terminal portion of the fusion peptide can be solvent-exposed. These results reveal the fusion peptide to be a neutralizing antibody epitope and thus a target for vaccine design.

-	~~Authors~~:	+	Fusion peptide of HIV-1 as a site of vulnerability to neutralizing antibody.,Kong R, Xu K, Zhou T, Acharya P, Lemmin T, Liu K, Ozorowski G, Soto C, Taft JD, Bailer RT, Cale EM, Chen L, Choi CW, Chuang GY, Doria-Rose NA, Druz A, Georgiev IS, Gorman J, Huang J, Joyce MG, Louder MK, Ma X, McKee K, O'Dell S, Pancera M, Yang Y, Blanchard SC, Mothes W, Burton DR, Koff WC, Connors M, Ward AB, Kwong PD, Mascola JR Science. 2016 May 13;352(6287):828-33. doi: 10.1126/science.aae0474. PMID:27174988<ref>PMID:27174988</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5i8c" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kwong, P D]]
		+	[[Category: Liu, K]]
		+	[[Category: Xu, K]]
		+	[[Category: Zhou, T]]
		+	[[Category: Antibody]]
		+	[[Category: Envelope]]
		+	[[Category: Fusion peptide]]
		+	[[Category: Hiv-1]]
		+	[[Category: Immune system]]
		+	[[Category: Neutralizing]]
		+	[[Category: Trimer]]

OCA at 14:14, 15 May 2016

OCA — Sun, 15 May 2016 14:14:09 GMT

←Older revision		Revision as of 14:14, 15 May 2016
Line 3:		Line 3:
	The entry 5i8c is ON HOLD until Paper Publication		The entry 5i8c is ON HOLD until Paper Publication

-	Authors: ~~Xu, K., Zhou, T., Liu, K., Kwong, P.D.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Kwong, P.D]]
-	[[Category: Zhou, T]]
-	[[Category: Xu, K]]
-	[[Category: Liu, K]]

OCA at 13:30, 2 March 2016

OCA — Wed, 02 Mar 2016 13:30:56 GMT

←Older revision		Revision as of 13:30, 2 March 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5i8c is ON HOLD	+	The entry 5i8c is ON HOLD until Paper Publication

	Authors: Xu, K., Zhou, T., Liu, K., Kwong, P.D.		Authors: Xu, K., Zhou, T., Liu, K., Kwong, P.D.

OCA: Protected "5i8c" [edit=sysop:move=sysop]

OCA — Fri, 26 Feb 2016 16:58:35 GMT

Protected "5i8c" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:58, 26 February 2016

OCA: New page: '''Unreleased structure''' The entry 5i8c is ON HOLD Authors: Xu, K., Zhou, T., Liu, K., Kwong, P.D. Description: Category: Unreleased Structures Category: Kwong, P.D [[Catego...

OCA — Fri, 26 Feb 2016 16:58:33 GMT

New page: '''Unreleased structure''' The entry 5i8c is ON HOLD Authors: Xu, K., Zhou, T., Liu, K., Kwong, P.D. Description: Category: Unreleased Structures Category: Kwong, P.D [[Catego...

New page

'''Unreleased structure'''

The entry 5i8c is ON HOLD

Authors: Xu, K., Zhou, T., Liu, K., Kwong, P.D.

Description:
[[Category: Unreleased Structures]]
[[Category: Kwong, P.D]]
[[Category: Zhou, T]]
[[Category: Xu, K]]
[[Category: Liu, K]]