OCA at 07:23, 8 September 2022

2022-09-08T07:23:38Z

←Older revision		Revision as of 07:23, 8 September 2022
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-	====	+	==XG005-bound SARS-CoV-2 S==
-	<StructureSection load='7v26' size='340' side='right'caption='[[7v26]]' scene=''>	+	<StructureSection load='7v26' size='340' side='right'caption='[[7v26]], [[Resolution\|resolution]] 3.85Å' 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'>[[7v26]] is a 9 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=7V26 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V26 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=7v26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v26 OCA], [https://pdbe.org/7v26 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v26 RCSB], [https://www.ebi.ac.uk/pdbsum/7v26 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v26 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=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=7v26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v26 OCA], [https://pdbe.org/7v26 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v26 RCSB], [https://www.ebi.ac.uk/pdbsum/7v26 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v26 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 ==
		+	New threats posed by the emerging circulating variants of SARS-CoV-2 highlight the need to find conserved neutralizing epitopes for therapeutic antibodies and efficient vaccine design. Here, we identified a receptor-binding domain (RBD)-binding antibody, XG014, which potently neutralizes beta-coronavirus lineage B (beta-CoV-B), including SARS-CoV-2, its circulating variants, SARS-CoV and bat SARSr-CoV WIV1. Interestingly, antibody family members competing with XG014 binding show reduced levels of cross-reactivity and induce antibody-dependent SARS-CoV-2 spike (S) protein-mediated cell-cell fusion, suggesting a unique mode of recognition by XG014. Structural analyses reveal that XG014 recognizes a conserved epitope outside the ACE2 binding site and completely locks RBD in the non-functional "down" conformation, while its family member XG005 directly competes with ACE2 binding and position the RBD "up". Single administration of XG014 is effective in protection against and therapy of SARS-CoV-2 infection in vivo. Our findings suggest the potential to develop XG014 as pan-beta-CoV-B therapeutics and the importance of the XG014 conserved antigenic epitope for designing broadly protective vaccines against beta-CoV-B and newly emerging SARS-CoV-2 variants of concern.
		+
		+	An ultrapotent pan-beta-coronavirus lineage B (beta-CoV-B) neutralizing antibody locks the receptor-binding domain in closed conformation by targeting its conserved epitope.,Liu Z, Xu W, Chen Z, Fu W, Zhan W, Gao Y, Zhou J, Zhou Y, Wu J, Wang Q, Zhang X, Hao A, Wu W, Zhang Q, Li Y, Fan K, Chen R, Jiang Q, Mayer CT, Schoofs T, Xie Y, Jiang S, Wen Y, Yuan Z, Wang K, Lu L, Sun L, Wang Q Protein Cell. 2022 Sep;13(9):655-675. doi: 10.1007/s13238-021-00871-6. Epub 2021 , Sep 23. PMID:34554412<ref>PMID:34554412</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7v26" style="background-color:#fffaf0;"></div>
		+	== 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: Chen ZG]]
		+	[[Category: Sun L]]
		+	[[Category: Zhan WQ]]
		+	[[Category: Zhang X]]

OCA at 16:34, 20 October 2021

2021-10-20T16:34:11Z

←Older revision		Revision as of 16:34, 20 October 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7v26 ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7v26' size='340' side='right'caption='[[7v26]]' 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 [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=7v26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v26 OCA], [https://pdbe.org/7v26 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v26 RCSB], [https://www.ebi.ac.uk/pdbsum/7v26 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v26 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 05:22, 25 August 2021

2021-08-25T05:22:27Z

←Older revision		Revision as of 05:22, 25 August 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7v26 is ON HOLD	+	The entry 7v26 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7v26" [edit=sysop:move=sysop]

2021-08-18T05:13:14Z

Protected "7v26" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:13, 18 August 2021

OCA: New page: '''Unreleased structure''' The entry 7v26 is ON HOLD Authors: Description: Category: Unreleased Structures

2021-08-18T05:13:13Z

New page: '''Unreleased structure''' The entry 7v26 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7v26 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7v26 - Revision history

OCA at 07:23, 8 September 2022

OCA at 16:34, 20 October 2021

OCA at 05:22, 25 August 2021

OCA: Protected "7v26" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7v26 is ON HOLD Authors: Description: Category: Unreleased Structures