6xdg - Revision history

OCA at 07:11, 2 September 2020

OCA — Wed, 02 Sep 2020 07:11:09 GMT

←Older revision		Revision as of 07:11, 2 September 2020
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	<StructureSection load='6xdg' size='340' side='right'caption='[[6xdg]], [[Resolution\|resolution]] 3.90Å' scene=''>		<StructureSection load='6xdg' size='340' side='right'caption='[[6xdg]], [[Resolution\|resolution]] 3.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6xdg]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/2019-ncov 2019-ncov], [http://en.wikipedia.org/wiki/Human Human~~] and [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XDG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6XDG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xdg]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/2019-ncov 2019-ncov] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XDG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6XDG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">S, 2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2697049 2019-nCoV])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">S, 2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2697049 2019-nCoV])</td></tr>
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	[[Category: Human]]		[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lk3 transgenic mice]]
	[[Category: Franklin, M C]]		[[Category: Franklin, M C]]
	[[Category: Hernandez, A Romero]]		[[Category: Hernandez, A Romero]]

OCA at 14:43, 8 July 2020

OCA — Wed, 08 Jul 2020 14:43:12 GMT

←Older revision		Revision as of 14:43, 8 July 2020
Line 1:		Line 1:

	==Complex of SARS-CoV-2 receptor binding domain with the Fab fragments of two neutralizing antibodies==		==Complex of SARS-CoV-2 receptor binding domain with the Fab fragments of two neutralizing antibodies==
-	<StructureSection load='6xdg' size='340' side='right'caption='[[6xdg]]' scene=''>	+	<StructureSection load='6xdg' size='340' side='right'caption='[[6xdg]], [[Resolution\|resolution]] 3.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XDG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6XDG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xdg]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/2019-ncov 2019-ncov], [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XDG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6XDG FirstGlance]. <br>
-	</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=6xdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xdg OCA], [http://pdbe.org/6xdg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6xdg RCSB], [http://www.ebi.ac.uk/pdbsum/6xdg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6xdg ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">S, 2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2697049 2019-nCoV])</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=6xdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xdg OCA], [http://pdbe.org/6xdg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6xdg RCSB], [http://www.ebi.ac.uk/pdbsum/6xdg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6xdg ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SPIKE_SARS2 SPIKE_SARS2]] attaches the virion to the cell membrane by interacting with host receptor, initiating the infection (By similarity). Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32075877, PubMed:32155444). Uses also human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes.[HAMAP-Rule:MF_04099]<ref>PMID:32075877</ref> <ref>PMID:32142651</ref> <ref>PMID:32155444</ref> mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, 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.[HAMAP-Rule:MF_04099] Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.[HAMAP-Rule:MF_04099]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Neutralizing antibodies have become an important tool in treating infectious diseases. Recently, two separate approaches yielded successful antibody treatments for Ebola - one from genetically-humanized mice, and the other from a human survivor. Here, we describe parallel efforts using both humanized mice and convalescent patients to generate antibodies against the SARS-CoV-2 spike protein, yielding a large collection of fully-human antibodies that were characterized for binding, neutralization and three dimensional structure. Based on these criteria, we selected pairs of highly-potent individual antibodies that simultaneously bind the receptor-binding domain of the spike protein, providing ideal partners for a therapeutic antibody cocktail that aims to decrease the potential for virus escape mutants that might arise in response to selective pressure from a single antibody treatment.
		+
		+	Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail.,Hansen J, Baum A, Pascal KE, Russo V, Giordano S, Wloga E, Fulton BO, Yan Y, Koon K, Patel K, Chung KM, Hermann A, Ullman E, Cruz J, Rafique A, Huang T, Fairhurst J, Libertiny C, Malbec M, Lee WY, Welsh R, Farr G, Pennington S, Deshpande D, Cheng J, Watty A, Bouffard P, Babb R, Levenkova N, Chen C, Zhang B, Romero Hernandez A, Saotome K, Zhou Y, Franklin M, Sivapalasingam S, Lye DC, Weston S, Logue J, Haupt R, Frieman M, Chen G, Olson W, Murphy AJ, Stahl N, Yancopoulos GD, Kyratsous CA Science. 2020 Jun 15. pii: science.abd0827. doi: 10.1126/science.abd0827. PMID:32540901<ref>PMID:32540901</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6xdg" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: 2019-ncov]]
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Franklin MC]]	+	[[Category: Lk3 transgenic mice]]
-	[[Category: ~~Romero~~ Hernandez A]]	+	[[Category: Franklin, M C]]
-	[[Category: Saotome K]]	+	[[Category: Hernandez, A Romero]]
-	[[Category: Zhou Y]]	+	[[Category: Saotome, K]]
		+	[[Category: Zhou, Y]]
		+	[[Category: Antiviral]]
		+	[[Category: Sars-cov-2]]
		+	[[Category: Therapeutic antibody]]
		+	[[Category: Viral protein-immune system complex]]

OCA at 06:31, 25 June 2020

OCA — Thu, 25 Jun 2020 06:31:27 GMT

←Older revision		Revision as of 06:31, 25 June 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6xdg is ~~ON HOLD~~	+	==Complex of SARS-CoV-2 receptor binding domain with the Fab fragments of two neutralizing antibodies==
-		+	<StructureSection load='6xdg' size='340' side='right'caption='[[6xdg]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XDG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6XDG FirstGlance]. <br>
-	~~Description~~:	+	</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=6xdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xdg OCA], [http://pdbe.org/6xdg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6xdg RCSB], [http://www.ebi.ac.uk/pdbsum/6xdg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6xdg ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Franklin MC]]
		+	[[Category: Romero Hernandez A]]
		+	[[Category: Saotome K]]
		+	[[Category: Zhou Y]]

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

OCA — Wed, 17 Jun 2020 08:45:15 GMT

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

←Older revision

Revision as of 08:45, 17 June 2020

OCA: New page: '''Unreleased structure''' The entry 6xdg is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 17 Jun 2020 08:45:14 GMT

New page: '''Unreleased structure''' The entry 6xdg is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6xdg is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]