OCA at 07:42, 9 November 2022

OCA — Wed, 09 Nov 2022 07:42:53 GMT

←Older revision		Revision as of 07:42, 9 November 2022
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-	====	+	==Cryo-EM structure of prefusion SARS-CoV-2 spike glycoprotein in complex with 910-30 Fab==
-	<StructureSection load='7ks9' size='340' side='right'caption='[[7ks9]]' scene=''>	+	<StructureSection load='7ks9' size='340' side='right'caption='[[7ks9]], [[Resolution\|resolution]] 4.75Å' 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'>[[7ks9]] is a 5 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=7KS9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KS9 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=7ks9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ks9 OCA], [https://pdbe.org/7ks9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ks9 RCSB], [https://www.ebi.ac.uk/pdbsum/7ks9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ks9 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=7ks9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ks9 OCA], [https://pdbe.org/7ks9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ks9 RCSB], [https://www.ebi.ac.uk/pdbsum/7ks9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ks9 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 ==
		+	Understanding mechanisms of protective antibody recognition can inform vaccine and therapeutic strategies against SARS-CoV-2. We report a monoclonal antibody, 910-30, targeting the SARS-CoV-2 receptor-binding site for ACE2 as a member of a public antibody response encoded by IGHV3-53/IGHV3-66 genes. Sequence and structural analyses of 910-30 and related antibodies explore how class recognition features correlate with SARS-CoV-2 neutralization. Cryo-EM structures of 910-30 bound to the SARS-CoV-2 spike trimer reveal binding interactions and its ability to disassemble spike. Despite heavy-chain sequence similarity, biophysical analyses of IGHV3-53/3-66-encoded antibodies highlight the importance of native heavy:light pairings for ACE2-binding competition and SARS-CoV-2 neutralization. We develop paired heavy:light class sequence signatures and determine antibody precursor prevalence to be approximately 1 in 44,000 human B cells, consistent with public antibody identification in several convalescent COVID-19 patients. These class signatures reveal genetic, structural, and functional immune features that are helpful in accelerating antibody-based medical interventions for SARS-CoV-2.
		+
		+	Paired heavy- and light-chain signatures contribute to potent SARS-CoV-2 neutralization in public antibody responses.,Banach BB, Cerutti G, Fahad AS, Shen CH, Oliveira De Souza M, Katsamba PS, Tsybovsky Y, Wang P, Nair MS, Huang Y, Francino-Urdaniz IM, Steiner PJ, Gutierrez-Gonzalez M, Liu L, Lopez Acevedo SN, Nazzari AF, Wolfe JR, Luo Y, Olia AS, Teng IT, Yu J, Zhou T, Reddem ER, Bimela J, Pan X, Madan B, Laflin AD, Nimrania R, Yuen KY, Whitehead TA, Ho DD, Kwong PD, Shapiro L, DeKosky BJ Cell Rep. 2021 Oct 5;37(1):109771. doi: 10.1016/j.celrep.2021.109771. Epub 2021, Sep 28. PMID:34587480<ref>PMID:34587480</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7ks9" 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: Cerutti G]]
		+	[[Category: Shapiro L]]

OCA at 11:04, 10 February 2021

OCA — Wed, 10 Feb 2021 11:04:18 GMT

←Older revision		Revision as of 11:04, 10 February 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7ks9 ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7ks9' size='340' side='right'caption='[[7ks9]]' 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=7ks9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ks9 OCA], [https://pdbe.org/7ks9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ks9 RCSB], [https://www.ebi.ac.uk/pdbsum/7ks9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ks9 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 05:26, 30 December 2020

OCA — Wed, 30 Dec 2020 05:26:14 GMT

←Older revision		Revision as of 05:26, 30 December 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7ks9 is ON HOLD	+	The entry 7ks9 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7ks9" [edit=sysop:move=sysop]

OCA — Wed, 02 Dec 2020 05:50:22 GMT

Protected "7ks9" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:50, 2 December 2020

OCA: New page: '''Unreleased structure''' The entry 7ks9 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 02 Dec 2020 05:50:20 GMT

New page: '''Unreleased structure''' The entry 7ks9 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7ks9 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7ks9 - Revision history

OCA at 07:42, 9 November 2022

OCA at 11:04, 10 February 2021

OCA at 05:26, 30 December 2020

OCA: Protected "7ks9" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7ks9 is ON HOLD Authors: Description: Category: Unreleased Structures