7jmw - Revision history

OCA at 15:07, 18 October 2023

OCA — Wed, 18 Oct 2023 15:07:01 GMT

←Older revision		Revision as of 15:07, 18 October 2023
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-	====	+	==Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with cross-neutralizing antibody COVA1-16 Fab==
-	<StructureSection load='7jmw' size='340' side='right'caption='[[7jmw]]' scene=''>	+	<StructureSection load='7jmw' size='340' side='right'caption='[[7jmw]], [[Resolution\|resolution]] 2.89Å' 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'>[[7jmw]] 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_coronavirus_2 Severe acute respiratory syndrome coronavirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JMW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JMW 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=7jmw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jmw OCA], [https://pdbe.org/7jmw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jmw RCSB], [https://www.ebi.ac.uk/pdbsum/7jmw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jmw 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]] 2.89Å</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></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=7jmw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jmw OCA], [https://pdbe.org/7jmw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jmw RCSB], [https://www.ebi.ac.uk/pdbsum/7jmw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jmw ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://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 ==
		+	Most antibodies isolated from individuals with coronavirus disease 2019 (COVID-19) are specific to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, COVA1-16 is a relatively rare antibody that also cross-neutralizes SARS-CoV. Here, we determined a crystal structure of the COVA1-16 antibody fragment (Fab) with the SARS-CoV-2 receptor-binding domain (RBD) and negative-stain electron microscopy reconstructions with the spike glycoprotein trimer to elucidate the structural basis of its cross-reactivity. COVA1-16 binds a highly conserved epitope on the SARS-CoV-2 RBD, mainly through a long complementarity-determining region (CDR) H3, and competes with the angiotensin-converting enzyme 2 (ACE2) receptor because of steric hindrance rather than epitope overlap. COVA1-16 binds to a flexible up conformation of the RBD on the spike and relies on antibody avidity for neutralization. These findings, along with the structural and functional rationale for epitope conservation, provide insights for development of more universal SARS-like coronavirus vaccines and therapies.
		+
		+	Cross-Neutralization of a SARS-CoV-2 Antibody to a Functionally Conserved Site Is Mediated by Avidity.,Liu H, Wu NC, Yuan M, Bangaru S, Torres JL, Caniels TG, van Schooten J, Zhu X, Lee CD, Brouwer PJM, van Gils MJ, Sanders RW, Ward AB, Wilson IA Immunity. 2020 Dec 15;53(6):1272-1280.e5. doi: 10.1016/j.immuni.2020.10.023. Epub , 2020 Nov 25. PMID:33242394<ref>PMID:33242394</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7jmw" 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 coronavirus 2]]
		+	[[Category: Liu H]]
		+	[[Category: Wilson IA]]
		+	[[Category: Wu NC]]
		+	[[Category: Yuan M]]
		+	[[Category: Zhu X]]

OCA at 07:32, 9 February 2022

OCA — Wed, 09 Feb 2022 07:32:07 GMT

←Older revision		Revision as of 07:32, 9 February 2022
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	<StructureSection load='7jmw' size='340' side='right'caption='[[7jmw]]' scene=''>		<StructureSection load='7jmw' size='340' side='right'caption='[[7jmw]]' 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=7jmw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jmw OCA], [~~http~~://pdbe.org/7jmw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7jmw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7jmw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7jmw 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=7jmw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jmw OCA], [https://pdbe.org/7jmw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jmw RCSB], [https://www.ebi.ac.uk/pdbsum/7jmw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jmw ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 05:52, 14 October 2020

OCA — Wed, 14 Oct 2020 05:52:53 GMT

←Older revision		Revision as of 05:52, 14 October 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7jmw ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7jmw' size='340' side='right'caption='[[7jmw]]' scene=''>
-	~~Authors~~:	+	== 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~~:	+	</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=7jmw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jmw OCA], [http://pdbe.org/7jmw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7jmw RCSB], [http://www.ebi.ac.uk/pdbsum/7jmw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7jmw ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 04:48, 19 August 2020

OCA — Wed, 19 Aug 2020 04:48:43 GMT

←Older revision		Revision as of 04:48, 19 August 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7jmw is ON HOLD	+	The entry 7jmw is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Wed, 12 Aug 2020 08:30:52 GMT

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

←Older revision

Revision as of 08:30, 12 August 2020

OCA: New page: '''Unreleased structure''' The entry 7jmw is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 12 Aug 2020 08:30:51 GMT

New page: '''Unreleased structure''' The entry 7jmw is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7jmw is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]