7tp3 - Revision history

OCA at 17:06, 18 October 2023

OCA — Wed, 18 Oct 2023 17:06:28 GMT

←Older revision		Revision as of 17:06, 18 October 2023
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	==Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody K288.2==		==Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody K288.2==
-	<StructureSection load='7tp3' size='340' side='right'caption='[[7tp3]]' scene=''>	+	<StructureSection load='7tp3' size='340' side='right'caption='[[7tp3]], [[Resolution\|resolution]] 2.33Å' 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=7TP3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TP3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7tp3]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Macaca_mulatta Macaca mulatta] 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=7TP3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TP3 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=7tp3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tp3 OCA], [https://pdbe.org/7tp3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tp3 RCSB], [https://www.ebi.ac.uk/pdbsum/7tp3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tp3 ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.33Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</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=7tp3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tp3 OCA], [https://pdbe.org/7tp3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tp3 RCSB], [https://www.ebi.ac.uk/pdbsum/7tp3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tp3 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 ==
		+	To prepare for future coronavirus (CoV) pandemics, it is desirable to generate vaccines capable of eliciting broadly neutralizing antibody responses to CoVs. Here, we show that immunization of macaques with SARS-CoV-2 spike (S) protein with a two-shot protocol generated potent serum receptor binding domain cross-neutralizing antibody responses to both SARS-CoV-2 and SARS-CoV-1. Furthermore, responses were equally effective against most SARS-CoV-2 variants of concern (VOCs) and some were highly effective against Omicron. This result contrasts with human infection or many two-shot vaccination protocols where responses were typically more SARS-CoV-2 specific and where VOCs were less well neutralized. Structural studies showed that cloned macaque neutralizing antibodies, particularly using a given heavy chain germline gene, recognized a relatively conserved region proximal to the angiotensin converting enzyme 2 receptor binding site (RBS), whereas many frequently elicited human neutralizing antibodies targeted more variable epitopes overlapping the RBS. B cell repertoire differences between humans and macaques appeared to influence the vaccine response. The macaque neutralizing antibodies identified a pan-SARS-related virus epitope region less well targeted by human antibodies that could be exploited in rational vaccine design.
		+
		+	Broadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques.,He WT, Yuan M, Callaghan S, Musharrafieh R, Song G, Silva M, Beutler N, Lee WH, Yong P, Torres JL, Melo M, Zhou P, Zhao F, Zhu X, Peng L, Huang D, Anzanello F, Ricketts J, Parren M, Garcia E, Ferguson M, Rinaldi W, Rawlings SA, Nemazee D, Smith DM, Briney B, Safonova Y, Rogers TF, Dan JM, Zhang Z, Weiskopf D, Sette A, Crotty S, Irvine DJ, Ward AB, Wilson IA, Burton DR, Andrabi R Sci Transl Med. 2022 Aug 10;14(657):eabl9605. doi: 10.1126/scitranslmed.abl9605. , Epub 2022 Aug 10. PMID:35947674<ref>PMID:35947674</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7tp3" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Macaca mulatta]]
		+	[[Category: Severe acute respiratory syndrome coronavirus 2]]
	[[Category: Wilson IA]]		[[Category: Wilson IA]]
	[[Category: Yuan M]]		[[Category: Yuan M]]
	[[Category: Zhu X]]		[[Category: Zhu X]]

OCA at 11:09, 31 August 2022

OCA — Wed, 31 Aug 2022 11:09:35 GMT

←Older revision		Revision as of 11:09, 31 August 2022
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-	====	+	==Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody K288.2==
	<StructureSection load='7tp3' size='340' side='right'caption='[[7tp3]]' scene=''>		<StructureSection load='7tp3' size='340' side='right'caption='[[7tp3]]' 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'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TP3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TP3 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=7tp3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tp3 OCA], [https://pdbe.org/7tp3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tp3 RCSB], [https://www.ebi.ac.uk/pdbsum/7tp3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tp3 ProSAT]</span></td></tr>		</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=7tp3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tp3 OCA], [https://pdbe.org/7tp3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tp3 RCSB], [https://www.ebi.ac.uk/pdbsum/7tp3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tp3 ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Wilson IA]]
		+	[[Category: Yuan M]]
		+	[[Category: Zhu X]]

OCA at 07:44, 23 February 2022

OCA — Wed, 23 Feb 2022 07:44:33 GMT

←Older revision		Revision as of 07:44, 23 February 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7tp3 ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7tp3' size='340' side='right'caption='[[7tp3]]' 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=7tp3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tp3 OCA], [https://pdbe.org/7tp3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tp3 RCSB], [https://www.ebi.ac.uk/pdbsum/7tp3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tp3 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA: Protected "7tp3" [edit=sysop:move=sysop]

OCA — Wed, 02 Feb 2022 05:40:04 GMT

Protected "7tp3" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:40, 2 February 2022

OCA: New page: '''Unreleased structure''' The entry 7tp3 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 02 Feb 2022 05:40:02 GMT

New page: '''Unreleased structure''' The entry 7tp3 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7tp3 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]