6snd - Revision history

OCA at 09:27, 27 November 2019

OCA — Wed, 27 Nov 2019 09:27:31 GMT

←Older revision		Revision as of 09:27, 27 November 2019
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	<StructureSection load='6snd' size='340' side='right'caption='[[6snd]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='6snd' size='340' side='right'caption='[[6snd]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6snd]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SND OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SND FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6snd]] is a 6 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=6SND OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SND FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPV:DODECYL+2-(TRIMETHYLAMMONIO)ETHYL+PHOSPHATE'>DPV</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PC:PHOSPHOCHOLINE'>PC</scene>, <scene name='pdbligand=PSF:1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE'>PSF</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPV:DODECYL+2-(TRIMETHYLAMMONIO)ETHYL+PHOSPHATE'>DPV</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PC:PHOSPHOCHOLINE'>PC</scene>, <scene name='pdbligand=PSF:1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE'>PSF</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=6snd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6snd OCA], [http://pdbe.org/6snd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6snd RCSB], [http://www.ebi.ac.uk/pdbsum/6snd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6snd 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=6snd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6snd OCA], [http://pdbe.org/6snd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6snd RCSB], [http://www.ebi.ac.uk/pdbsum/6snd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6snd ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Caillat, C]]		[[Category: Caillat, C]]

OCA at 06:51, 6 November 2019

OCA — Wed, 06 Nov 2019 06:51:35 GMT

←Older revision		Revision as of 06:51, 6 November 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6snd is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==crystal structure of LN01 Fab in complex with an HIV-1 gp41 peptide==
		+	<StructureSection load='6snd' size='340' side='right'caption='[[6snd]], [[Resolution\|resolution]] 3.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6snd]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SND OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SND FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPV:DODECYL+2-(TRIMETHYLAMMONIO)ETHYL+PHOSPHATE'>DPV</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PC:PHOSPHOCHOLINE'>PC</scene>, <scene name='pdbligand=PSF:1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE'>PSF</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=6snd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6snd OCA], [http://pdbe.org/6snd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6snd RCSB], [http://www.ebi.ac.uk/pdbsum/6snd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6snd ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/G3DH64_9HIV1 G3DH64_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;">
		+	== Publication Abstract from PubMed ==
		+	Potent and broadly neutralizing antibodies (bnAbs) are the hallmark of HIV-1 protection by vaccination. The membrane-proximal external region (MPER) of the HIV-1 gp41 fusion protein is targeted by the most broadly reactive HIV-1 neutralizing antibodies. Here, we examine the structural and molecular mechansims of neutralization by anti-MPER bnAb, LN01, which was isolated from lymph-node-derived germinal center B cells of an elite controller and exhibits broad neutralization breadth. LN01 engages both MPER and the transmembrane (TM) region, which together form a continuous helix in complex with LN01. The tilted TM orientation allows LN01 to interact simultaneously with the peptidic component of the MPER epitope and membrane via two specific lipid binding sites of the antibody paratope. Although LN01 carries a high load of somatic mutations, most key residues interacting with the MPER epitope and lipids are germline encoded, lending support for the LN01 epitope as a candidate for lineage-based vaccine development.

-	~~Authors~~:	+	Structural Basis for Broad HIV-1 Neutralization by the MPER-Specific Human Broadly Neutralizing Antibody LN01.,Pinto D, Fenwick C, Caillat C, Silacci C, Guseva S, Dehez F, Chipot C, Barbieri S, Minola A, Jarrossay D, Tomaras GD, Shen X, Riva A, Tarkowski M, Schwartz O, Bruel T, Dufloo J, Seaman MS, Montefiori DC, Lanzavecchia A, Corti D, Pantaleo G, Weissenhorn W Cell Host Microbe. 2019 Oct 22. pii: S1931-3128(19)30483-4. doi:, 10.1016/j.chom.2019.09.016. PMID:31653484<ref>PMID:31653484</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6snd" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Caillat, C]]
		+	[[Category: Corti, D]]
		+	[[Category: Fenwick, C]]
		+	[[Category: Pantaleo, G]]
		+	[[Category: Pinto, D]]
		+	[[Category: Weissenhorn, W]]
		+	[[Category: Antibody]]
		+	[[Category: Complex]]
		+	[[Category: Gp41]]
		+	[[Category: Immune system]]
		+	[[Category: Mper]]

OCA: Protected "6snd" [edit=sysop:move=sysop]

OCA — Wed, 02 Oct 2019 07:26:11 GMT

Protected "6snd" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:26, 2 October 2019

OCA: New page: '''Unreleased structure''' The entry 6snd is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 02 Oct 2019 07:26:10 GMT

New page: '''Unreleased structure''' The entry 6snd is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6snd is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]