7jn5 - Revision history

OCA at 15:07, 18 October 2023

OCA — Wed, 18 Oct 2023 15:07:06 GMT

←Older revision		Revision as of 15:07, 18 October 2023
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-	====	+	==Crystal structure of SARS-CoV receptor binding domain in complex with human antibody CR3022==
-	<StructureSection load='7jn5' size='340' side='right'caption='[[7jn5]]' scene=''>	+	<StructureSection load='7jn5' size='340' side='right'caption='[[7jn5]], [[Resolution\|resolution]] 2.71Å' 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= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7jn5]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome-related_coronavirus Severe acute respiratory syndrome-related coronavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JN5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JN5 FirstGlance]. <br>
-	</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=7jn5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jn5 OCA], [https://pdbe.org/7jn5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jn5 RCSB], [https://www.ebi.ac.uk/pdbsum/7jn5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jn5 ProSAT]</span></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]] 2.705Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=7jn5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jn5 OCA], [https://pdbe.org/7jn5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jn5 RCSB], [https://www.ebi.ac.uk/pdbsum/7jn5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jn5 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SPIKE_SARS SPIKE_SARS] May down-regulate host tetherin (BST2) by lysosomal degradation, thereby counteracting its antiviral activity.<ref>PMID:31199522</ref> Attaches the virion to the cell membrane by interacting with host receptor, initiating the infection (By similarity). Binding to human ACE2 and CLEC4M/DC-SIGNR receptors and internalization of the virus into the endosomes of the host cell induces conformational changes in the S glycoprotein. Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membrane fusion within endosomes.[HAMAP-Rule:MF_04099]<ref>PMID:14670965</ref> <ref>PMID:15496474</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]<ref>PMID:19321428</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Epitopes that are conserved among SARS-like coronaviruses are attractive targets for design of cross-reactive vaccines and therapeutics. CR3022 is a SARS-CoV neutralizing antibody to a highly conserved epitope on the receptor binding domain (RBD) on the spike protein that is able to cross-react with SARS-CoV-2, but with lower affinity. Using x-ray crystallography, mutagenesis, and binding experiments, we illustrate that of four amino acid differences in the CR3022 epitope between SARS-CoV-2 and SARS-CoV, a single mutation P384A fully determines the affinity difference. CR3022 does not neutralize SARS-CoV-2, but the increased affinity to SARS-CoV-2 P384A mutant now enables neutralization with a similar potency to SARS-CoV. We further investigated CR3022 interaction with the SARS-CoV spike protein by negative-stain EM and cryo-EM. Three CR3022 Fabs bind per trimer with the RBD observed in different up-conformations due to considerable flexibility of the RBD. In one of these conformations, quaternary interactions are made by CR3022 to the N-terminal domain (NTD) of an adjacent subunit. Overall, this study provides insights into antigenic variation and potential cross-neutralizing epitopes on SARS-like viruses.
		+
		+	A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody.,Wu NC, Yuan M, Bangaru S, Huang D, Zhu X, Lee CD, Turner HL, Peng L, Yang L, Burton DR, Nemazee D, Ward AB, Wilson IA PLoS Pathog. 2020 Dec 4;16(12):e1009089. doi: 10.1371/journal.ppat.1009089. , eCollection 2020 Dec. PMID:33275640<ref>PMID:33275640</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7jn5" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Z-~~disk~~]]	+	[[Category: Severe acute respiratory syndrome-related coronavirus]]
		+	[[Category: Wilson IA]]
		+	[[Category: Wu NC]]
		+	[[Category: Yuan M]]
		+	[[Category: Zhu X]]

OCA at 09:39, 12 May 2021

OCA — Wed, 12 May 2021 09:39:09 GMT

←Older revision		Revision as of 09:39, 12 May 2021
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	<StructureSection load='7jn5' size='340' side='right'caption='[[7jn5]]' scene=''>		<StructureSection load='7jn5' size='340' side='right'caption='[[7jn5]]' 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= OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= 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=7jn5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jn5 OCA], [~~http~~://pdbe.org/7jn5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7jn5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7jn5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7jn5 ProSAT]</span></td></tr>	+	</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=7jn5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jn5 OCA], [https://pdbe.org/7jn5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jn5 RCSB], [https://www.ebi.ac.uk/pdbsum/7jn5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jn5 ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 20:38, 28 October 2020

OCA — Wed, 28 Oct 2020 20:38:26 GMT

←Older revision		Revision as of 20:38, 28 October 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7jn5 ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7jn5' size='340' side='right'caption='[[7jn5]]' scene=''>
-	~~Authors~~: ~~Wu, N~~.C.~~, Yuan, M~~.~~, Zhu, X~~.~~, Wilson, I~~.A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of SARS-CoV receptor binding domain in complex with human antibody CR3022~~	+	</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=7jn5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jn5 OCA], [http://pdbe.org/7jn5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7jn5 RCSB], [http://www.ebi.ac.uk/pdbsum/7jn5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7jn5 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: ~~Wilson, I~~.A]]	+	__TOC__
-	[~~[Category~~: ~~Zhu, X~~]]	+	</StructureSection>
-	[[Category: ~~Wu, N.C~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Yuan, M~~]]	+	[[Category: Z-disk]]

OCA: Protected "7jn5" [edit=sysop:move=sysop]

OCA — Wed, 12 Aug 2020 08:31:26 GMT

Protected "7jn5" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:31, 12 August 2020

OCA: New page: '''Unreleased structure''' The entry 7jn5 is ON HOLD until Paper Publication Authors: Wu, N.C., Yuan, M., Zhu, X., Wilson, I.A. Description: Crystal structure of SARS-CoV receptor bind...

OCA — Wed, 12 Aug 2020 08:31:25 GMT

New page: '''Unreleased structure''' The entry 7jn5 is ON HOLD until Paper Publication Authors: Wu, N.C., Yuan, M., Zhu, X., Wilson, I.A. Description: Crystal structure of SARS-CoV receptor bind...

New page

'''Unreleased structure'''

The entry 7jn5 is ON HOLD until Paper Publication

Authors: Wu, N.C., Yuan, M., Zhu, X., Wilson, I.A.

Description: Crystal structure of SARS-CoV receptor binding domain in complex with human antibody CR3022
[[Category: Unreleased Structures]]
[[Category: Wilson, I.A]]
[[Category: Zhu, X]]
[[Category: Wu, N.C]]
[[Category: Yuan, M]]