5u3o - Revision history

OCA at 13:19, 4 October 2023

OCA — Wed, 04 Oct 2023 13:19:21 GMT

←Older revision		Revision as of 13:19, 4 October 2023
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	==Crystal Structure of DH511.2_K3 Fab in Complex with HIV-1 gp41 MPER Peptide==		==Crystal Structure of DH511.2_K3 Fab in Complex with HIV-1 gp41 MPER Peptide==
-	<StructureSection load='5u3o' size='340' side='right' caption='[[5u3o]], [[Resolution\|resolution]] 1.76Å' scene=''>	+	<StructureSection load='5u3o' size='340' side='right'caption='[[5u3o]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5u3o]] 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=5U3O OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5U3O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5u3o]] 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=5U3O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5U3O FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5u3j\|5u3j]], [[5u3k\|5u3k]], [[5u3l\|5u3l]], [[5u3m\|5u3m]], [[5u3n\|5u3n]], [[5u3p\|5u3p]]</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]] 1.761Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">IgG Heavy Chain ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=9606 HUMAN]), IgG Light Chain ([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=5u3o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u3o OCA], [https://pdbe.org/5u3o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5u3o RCSB], [https://www.ebi.ac.uk/pdbsum/5u3o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5u3o 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=5u3o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u3o OCA], [~~http~~://pdbe.org/5u3o PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5u3o RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5u3o PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5u3o ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ENV_HV1B9 ENV_HV1B9] 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] 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] 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: ~~Haynes, B F~~]]	+	[[Category: Human immunodeficiency virus 1]]
-	[[Category: ~~Lougheed, C S~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Nicely, N I~~]]	+	[[Category: Haynes BF]]
-	[[Category: ~~Ofek, G~~]]	+	[[Category: Lougheed CS]]
-	[[Category: ~~Williams, L D~~]]	+	[[Category: Nicely NI]]
-	[[Category: ~~Wu, L~~]]	+	[[Category: Ofek G]]
-	[[Category: ~~Antibody~~]]	+	[[Category: Williams LD]]
-	[[Category: ~~Gp41]]~~	+	[[Category: Wu L]]
-	~~[[Category: Hiv-1]]~~	+
-	~~[[Category: Immune system-viral protein complex]]~~	+
-	~~[[Category: Mper]]~~	+
-	~~[[Category: Neutralizing~~]]	+

OCA at 10:20, 22 November 2017

OCA — Wed, 22 Nov 2017 10:20:32 GMT

←Older revision		Revision as of 10:20, 22 November 2017
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	<StructureSection load='5u3o' size='340' side='right' caption='[[5u3o]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='5u3o' size='340' side='right' caption='[[5u3o]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5u3o]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U3O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U3O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5u3o]] 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=5U3O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U3O FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5u3j\|5u3j]], [[5u3k\|5u3k]], [[5u3l\|5u3l]], [[5u3m\|5u3m]], [[5u3n\|5u3n]], [[5u3p\|5u3p]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5u3j\|5u3j]], [[5u3k\|5u3k]], [[5u3l\|5u3l]], [[5u3m\|5u3m]], [[5u3n\|5u3n]], [[5u3p\|5u3p]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IgG Heavy Chain ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), IgG Light Chain ([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=5u3o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u3o OCA], [http://pdbe.org/5u3o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u3o RCSB], [http://www.ebi.ac.uk/pdbsum/5u3o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u3o 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=5u3o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u3o OCA], [http://pdbe.org/5u3o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u3o RCSB], [http://www.ebi.ac.uk/pdbsum/5u3o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u3o ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Haynes, B F]]		[[Category: Haynes, B F]]
	[[Category: Lougheed, C S]]		[[Category: Lougheed, C S]]

OCA at 11:09, 24 August 2017

OCA — Thu, 24 Aug 2017 11:09:22 GMT

←Older revision		Revision as of 11:09, 24 August 2017
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	<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=5u3o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u3o OCA], [http://pdbe.org/5u3o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u3o RCSB], [http://www.ebi.ac.uk/pdbsum/5u3o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u3o 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=5u3o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u3o OCA], [http://pdbe.org/5u3o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u3o RCSB], [http://www.ebi.ac.uk/pdbsum/5u3o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u3o ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Induction of broadly neutralizing antibodies (bnAbs) is a goal of HIV-1 vaccine development. Antibody 10E8, reactive with the distal portion of the membrane-proximal external region (MPER) of HIV-1 gp41, is broadly neutralizing. However, the ontogeny of distal MPER antibodies and the relationship of memory B cell to plasma bnAbs are poorly understood. HIV-1-specific memory B cell flow sorting and proteomic identification of anti-MPER plasma antibodies from an HIV-1-infected individual were used to isolate broadly neutralizing distal MPER bnAbs of the same B cell clonal lineage. Structural analysis demonstrated that antibodies from memory B cells and plasma recognized the envelope gp41 bnAb epitope in a distinct orientation compared with other distal MPER bnAbs. The unmutated common ancestor of this distal MPER bnAb was autoreactive, suggesting lineage immune tolerance control. Construction of chimeric antibodies of memory B cell and plasma antibodies yielded a bnAb that potently neutralized most HIV-1 strains.
		+
		+	Potent and broad HIV-neutralizing antibodies in memory B cells and plasma.,Williams LD, Ofek G, Schatzle S, McDaniel JR, Lu X, Nicely NI, Wu L, Lougheed CS, Bradley T, Louder MK, McKee K, Bailer RT, O'Dell S, Georgiev IS, Seaman MS, Parks RJ, Marshall DJ, Anasti K, Yang G, Nie X, Tumba NL, Wiehe K, Wagh K, Korber B, Kepler TB, Munir Alam S, Morris L, Kamanga G, Cohen MS, Bonsignori M, Xia SM, Montefiori DC, Kelsoe G, Gao F, Mascola JR, Moody MA, Saunders KO, Liao HX, Tomaras GD, Georgiou G, Haynes BF Sci Immunol. 2017 Jan 27;2(7). pii: eaal2200. doi: 10.1126/sciimmunol.aal2200. PMID:28783671<ref>PMID:28783671</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5u3o" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:46, 10 March 2017

OCA — Fri, 10 Mar 2017 17:46:18 GMT

←Older revision		Revision as of 17:46, 10 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5u3o ~~is ON HOLD~~	+	==Crystal Structure of DH511.2_K3 Fab in Complex with HIV-1 gp41 MPER Peptide==
-		+	<StructureSection load='5u3o' size='340' side='right' caption='[[5u3o]], [[Resolution\|resolution]] 1.76Å' scene=''>
-	~~Authors~~: ~~Ofek, G~~., Wu, L., ~~Lougheed~~, C.S., ~~Williams, L~~.D., ~~Nicely~~, N.I., Haynes, B.F.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5u3o]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U3O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U3O FirstGlance]. <br>
-	~~Description~~: ~~Crystal Structure of DH511.2_K3 Fab in Complex with HIV-1 gp41 MPER Peptide~~	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5u3j\|5u3j]], [[5u3k\|5u3k]], [[5u3l\|5u3l]], [[5u3m\|5u3m]], [[5u3n\|5u3n]], [[5u3p\|5u3p]]</td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5u3o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u3o OCA], [http://pdbe.org/5u3o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u3o RCSB], [http://www.ebi.ac.uk/pdbsum/5u3o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u3o ProSAT]</span></td></tr>
-	[[Category: ~~Haynes~~, ~~B.F~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Haynes, B F]]
		+	[[Category: Lougheed, C S]]
		+	[[Category: Nicely, N I]]
		+	[[Category: Ofek, G]]
		+	[[Category: Williams, L D]]
	[[Category: Wu, L]]		[[Category: Wu, L]]
-	[[Category: ~~Ofek, G~~]]	+	[[Category: Antibody]]
-	[[Category: ~~Lougheed, C.S~~]]	+	[[Category: Gp41]]
-	[[Category: ~~Williams, L.D~~]]	+	[[Category: Hiv-1]]
-	[[Category: ~~Nicely, N.I~~]]	+	[[Category: Immune system-viral protein complex]]
		+	[[Category: Mper]]
		+	[[Category: Neutralizing]]

OCA: Protected "5u3o" [edit=sysop:move=sysop]

OCA — Thu, 15 Dec 2016 17:37:46 GMT

Protected "5u3o" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:37, 15 December 2016

OCA: New page: '''Unreleased structure''' The entry 5u3o is ON HOLD Authors: Ofek, G., Wu, L., Lougheed, C.S., Williams, L.D., Nicely, N.I., Haynes, B.F. Description: Crystal Structure of DH511.2_K3 ...

OCA — Thu, 15 Dec 2016 17:37:45 GMT

New page: '''Unreleased structure''' The entry 5u3o is ON HOLD Authors: Ofek, G., Wu, L., Lougheed, C.S., Williams, L.D., Nicely, N.I., Haynes, B.F. Description: Crystal Structure of DH511.2_K3 ...

New page

'''Unreleased structure'''

The entry 5u3o is ON HOLD

Authors: Ofek, G., Wu, L., Lougheed, C.S., Williams, L.D., Nicely, N.I., Haynes, B.F.

Description: Crystal Structure of DH511.2_K3 Fab in Complex with HIV-1 gp41 MPER Peptide
[[Category: Unreleased Structures]]
[[Category: Haynes, B.F]]
[[Category: Wu, L]]
[[Category: Ofek, G]]
[[Category: Lougheed, C.S]]
[[Category: Williams, L.D]]
[[Category: Nicely, N.I]]