OCA at 07:24, 16 March 2022

OCA — Wed, 16 Mar 2022 07:24:43 GMT

←Older revision		Revision as of 07:24, 16 March 2022
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	==Prototypic SARS-CoV-2 G614 spike (open form)==		==Prototypic SARS-CoV-2 G614 spike (open form)==
-	<StructureSection load='7tgx' size='340' side='right'caption='[[7tgx]]' scene=''>	+	<StructureSection load='7tgx' size='340' side='right'caption='[[7tgx]], [[Resolution\|resolution]] 3.20Å' 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=7TGX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TGX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7tgx]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TGX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TGX 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=7tgx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tgx OCA], [https://pdbe.org/7tgx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tgx RCSB], [https://www.ebi.ac.uk/pdbsum/7tgx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tgx 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=MAN:ALPHA-D-MANNOSE'>MAN</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=7tgx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tgx OCA], [https://pdbe.org/7tgx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tgx RCSB], [https://www.ebi.ac.uk/pdbsum/7tgx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tgx 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 ==
		+	The omicron variant of SARS-CoV-2 has been spreading rapidly across the globe. The virus-surface spike protein plays a critical role in the cell entry and immune evasion of SARS-CoV-2. Here we determined the 3.0 A cryo-EM structure of the omicron spike protein ectodomain. In contrast to the original strain of SARS-CoV-2 where the receptor-binding domain (RBD) of the spike protein takes a mixture of open ("standing up") and closed ("lying down") conformations, the omicron spike molecules are predominantly in the open conformation, with one upright RBD ready for receptor binding. The open conformation of the omicron spike is stabilized by enhanced inter-domain and inter-subunit packing, which involves new mutations in the omicron strain. Moreover, the omicron spike has undergone extensive mutations in RBD regions where known neutralizing antibodies target, allowing the omicron variant to escape immune surveillance aimed at the original viral strain. The stable open conformation of the omicron spike sheds light on the cell entry and immune evasion mechanisms of the omicron variant.
		+
		+	Cryo-EM structure of a SARS-CoV-2 omicron spike protein ectodomain.,Ye G, Liu B, Li F Nat Commun. 2022 Mar 3;13(1):1214. doi: 10.1038/s41467-022-28882-9. PMID:35241675<ref>PMID:35241675</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7tgx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Li F]]	+	[[Category: Li, F]]
-	[[Category: Liu B]]	+	[[Category: Liu, B]]
-	[[Category: Ye G]]	+	[[Category: Ye, G]]
		+	[[Category: Prototypic sars-cov-2 g614 spike]]
		+	[[Category: Viral protein]]

OCA at 06:08, 9 March 2022

OCA — Wed, 09 Mar 2022 06:08:04 GMT

←Older revision		Revision as of 06:08, 9 March 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7tgx is ~~ON HOLD until Paper Publication~~	+	==Prototypic SARS-CoV-2 G614 spike (open form)==
-		+	<StructureSection load='7tgx' size='340' side='right'caption='[[7tgx]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TGX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TGX 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=7tgx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tgx OCA], [https://pdbe.org/7tgx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tgx RCSB], [https://www.ebi.ac.uk/pdbsum/7tgx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tgx ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Li F]]
		+	[[Category: Liu B]]
		+	[[Category: Ye G]]

OCA at 09:06, 16 February 2022

OCA — Wed, 16 Feb 2022 09:06:49 GMT

←Older revision		Revision as of 09:06, 16 February 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 19 Jan 2022 06:01:41 GMT

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

←Older revision

Revision as of 06:01, 19 January 2022

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

OCA — Wed, 19 Jan 2022 06:01:40 GMT

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

New page

'''Unreleased structure'''

The entry 7tgx is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7tgx - Revision history

OCA at 07:24, 16 March 2022

OCA at 06:08, 9 March 2022

OCA at 09:06, 16 February 2022

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

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