OCA at 06:47, 21 November 2024

2024-11-21T06:47:04Z

← Older revision		Revision as of 06:47, 21 November 2024
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	====		==SARS-CoV-2 S NTD B.1.617.1 kappa variant S2X303 Local Refinement==
	<StructureSection load='7sof' size='340' side='right'caption='[[7sof]]' scene=''>		<StructureSection load='7sof' size='340' side='right'caption='[[7sof]], [[Resolution\|resolution]] 3.60Å' 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'>[[7sof]] 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=7SOF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7SOF 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=7sof FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7sof OCA], [https://pdbe.org/7sof PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7sof RCSB], [https://www.ebi.ac.uk/pdbsum/7sof PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7sof ProSAT]</span></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.6Å</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=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=7sof FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7sof OCA], [https://pdbe.org/7sof PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7sof RCSB], [https://www.ebi.ac.uk/pdbsum/7sof PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7sof 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 ==
			Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission leads to the emergence of variants, including the B.1.617.2 (Delta) variant of concern that is causing a new wave of infections and has become globally dominant. We show that these variants dampen the in vitro potency of vaccine-elicited serum neutralizing antibodies and provide a structural framework for describing their immune evasion. Mutations in the B.1.617.1 (Kappa) and Delta spike glycoproteins abrogate recognition by several monoclonal antibodies via alteration of key antigenic sites, including remodeling of the Delta amino-terminal domain. The angiotensin-converting enzyme 2 binding affinities of the Kappa and Delta receptor binding domains are comparable to the Wuhan-Hu-1 isolate, whereas B.1.617.2+ (Delta+) exhibits markedly reduced affinity.

			Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants.,McCallum M, Walls AC, Sprouse KR, Bowen JE, Rosen LE, Dang HV, De Marco A, Franko N, Tilles SW, Logue J, Miranda MC, Ahlrichs M, Carter L, Snell G, Pizzuto MS, Chu HY, Van Voorhis WC, Corti D, Veesler D Science. 2021 Dec 24;374(6575):1621-1626. doi: 10.1126/science.abl8506. Epub 2021 , Nov 9. PMID:34751595<ref>PMID:34751595</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7sof" 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: McCallum M]]
			[[Category: Veesler D]]

OCA at 13:40, 17 November 2021

2021-11-17T13:40:17Z

← Older revision		Revision as of 13:40, 17 November 2021
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	~~'''Unreleased structure'''~~

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

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

2021-11-10T05:16:45Z

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

← Older revision	Revision as of 05:16, 10 November 2021
(No difference)

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

2021-11-10T05:16:44Z

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

New page

'''Unreleased structure'''

The entry 7sof is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7sof - Revision history

OCA at 06:47, 21 November 2024

OCA at 13:40, 17 November 2021

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

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