8dlj - Revision history

OCA at 19:40, 7 September 2022

OCA — Wed, 07 Sep 2022 19:40:10 GMT

←Older revision		Revision as of 19:40, 7 September 2022
Line 1:		Line 1:

-	====	+	==Cryo-EM structure of SARS-CoV-2 Alpha (B.1.1.7) spike protein in complex with human ACE2==
-	<StructureSection load='8dlj' size='340' side='right'caption='[[8dlj]]' scene=''>	+	<StructureSection load='8dlj' size='340' side='right'caption='[[8dlj]], [[Resolution\|resolution]] 2.91Å' 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'>[[8dlj]] is a 4 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=8DLJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DLJ 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=8dlj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dlj OCA], [https://pdbe.org/8dlj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dlj RCSB], [https://www.ebi.ac.uk/pdbsum/8dlj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dlj 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=8dlj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dlj OCA], [https://pdbe.org/8dlj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dlj RCSB], [https://www.ebi.ac.uk/pdbsum/8dlj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dlj 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 ==
		+	Mutations in the spike glycoproteins of SARS-CoV-2 variants of concern have independently been shown to enhance aspects of spike protein fitness. Here, we describe an antibody fragment (VH ab6) that neutralizes all major variants including the recently emerged BA.1 and BA.2 Omicron subvariants, with a unique mode of binding revealed by cryo-EM studies. Further, we provide a comparative analysis of the mutational effects within previously emerged variant spikes and identify the structural role of mutations within the NTD and RBD in evading antibody neutralization. Our analysis shows that the highly mutated Gamma N-terminal domain exhibits considerable structural rearrangements, partially explaining its decreased neutralization by convalescent sera. Our results provide mechanistic insights into the structural, functional, and antigenic consequences of SARS-CoV-2 spike mutations and highlight a spike protein vulnerability that may be exploited to achieve broad protection against circulating variants.
		+
		+	SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.,Mannar D, Saville JW, Sun Z, Zhu X, Marti MM, Srivastava SS, Berezuk AM, Zhou S, Tuttle KS, Sobolewski MD, Kim A, Treat BR, Da Silva Castanha PM, Jacobs JL, Barratt-Boyes SM, Mellors JW, Dimitrov DS, Li W, Subramaniam S Nat Commun. 2022 Aug 18;13(1):4696. doi: 10.1038/s41467-022-32262-8. PMID:35982054<ref>PMID:35982054</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 8dlj" 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: Berezuk AM]]
		+	[[Category: Mannar D]]
		+	[[Category: Saville JW]]
		+	[[Category: Srivastava SS]]
		+	[[Category: Subramaniam S]]
		+	[[Category: Tuttle KS]]
		+	[[Category: Zhou S]]
		+	[[Category: Zhu X]]

OCA at 06:40, 31 August 2022

OCA — Wed, 31 Aug 2022 06:40:32 GMT

←Older revision		Revision as of 06:40, 31 August 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8dlj ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='8dlj' size='340' side='right'caption='[[8dlj]]' scene=''>
-	~~Authors~~: ~~Zhu, X~~.~~, Mannar, D~~.~~, Saville, J~~.W.~~, Srivastava, S~~.S.~~, Berezuk, A~~.M.~~, Zhou, S~~., ~~Tuttle, K~~.S.~~, Subramaniam, S~~.	+	== 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: Cryo~~-~~EM structure of SARS-CoV-2 Alpha (B.1.1.7) spike protein in complex with human ACE2~~	+	</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=8dlj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dlj OCA], [https://pdbe.org/8dlj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dlj RCSB], [https://www.ebi.ac.uk/pdbsum/8dlj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dlj ProSAT]</span></td></tr>
-	~~[[Category: Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: ~~Subramaniam, S~~]]	+	__TOC__
-	~~[[Category: Zhu~~, ~~X]]~~	+	</StructureSection>
-	[~~[Category~~: ~~Tuttle, K~~.S]]	+	[[Category: Large Structures]]
-	~~[[Category: Mannar~~, ~~D]]~~	+	[[Category: Z-disk]]
-	[~~[Category~~: ~~Saville, J~~.W]]	+
-	[~~[Category~~: ~~Zhou, S]~~]	+
-	[[Category: ~~Srivastava, S.S~~]]	+
-	[[Category: ~~Berezuk, A.M~~]]	+

OCA at 04:00, 18 August 2022

OCA — Thu, 18 Aug 2022 04:00:51 GMT

←Older revision		Revision as of 04:00, 18 August 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8dlj is ON HOLD	+	The entry 8dlj is ON HOLD until Paper Publication

	Authors: Zhu, X., Mannar, D., Saville, J.W., Srivastava, S.S., Berezuk, A.M., Zhou, S., Tuttle, K.S., Subramaniam, S.		Authors: Zhu, X., Mannar, D., Saville, J.W., Srivastava, S.S., Berezuk, A.M., Zhou, S., Tuttle, K.S., Subramaniam, S.

OCA: Protected "8dlj" [edit=sysop:move=sysop]

OCA — Wed, 13 Jul 2022 04:19:43 GMT

Protected "8dlj" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:19, 13 July 2022

OCA: New page: '''Unreleased structure''' The entry 8dlj is ON HOLD Authors: Zhu, X., Mannar, D., Saville, J.W., Srivastava, S.S., Berezuk, A.M., Zhou, S., Tuttle, K.S., Subramaniam, S. Description: ...

OCA — Wed, 13 Jul 2022 04:19:42 GMT

New page: '''Unreleased structure''' The entry 8dlj is ON HOLD Authors: Zhu, X., Mannar, D., Saville, J.W., Srivastava, S.S., Berezuk, A.M., Zhou, S., Tuttle, K.S., Subramaniam, S. Description: ...

New page

'''Unreleased structure'''

The entry 8dlj is ON HOLD

Authors: Zhu, X., Mannar, D., Saville, J.W., Srivastava, S.S., Berezuk, A.M., Zhou, S., Tuttle, K.S., Subramaniam, S.

Description: Cryo-EM structure of SARS-CoV-2 Alpha (B.1.1.7) spike protein in complex with human ACE2
[[Category: Unreleased Structures]]
[[Category: Subramaniam, S]]
[[Category: Zhu, X]]
[[Category: Tuttle, K.S]]
[[Category: Mannar, D]]
[[Category: Saville, J.W]]
[[Category: Zhou, S]]
[[Category: Srivastava, S.S]]
[[Category: Berezuk, A.M]]