OCA at 15:28, 18 October 2023

OCA — Wed, 18 Oct 2023 15:28:35 GMT

←Older revision		Revision as of 15:28, 18 October 2023
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-	====	+	==Crystal structure of SARS-CoV-2 spike protein receptor-binding domain complexed with a pre-pandemic antibody S-B8 Fab==
-	<StructureSection load='7kn3' size='340' side='right'caption='[[7kn3]]' scene=''>	+	<StructureSection load='7kn3' size='340' side='right'caption='[[7kn3]], [[Resolution\|resolution]] 2.25Å' 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'>[[7kn3]] is a 6 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=7KN3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KN3 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=7kn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kn3 OCA], [https://pdbe.org/7kn3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kn3 RCSB], [https://www.ebi.ac.uk/pdbsum/7kn3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kn3 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]] 2.251Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7kn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kn3 OCA], [https://pdbe.org/7kn3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kn3 RCSB], [https://www.ebi.ac.uk/pdbsum/7kn3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kn3 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 ==
		+	Combinatorial antibody libraries not only effectively reduce antibody discovery to a numbers game, but enable documentation of the history of antibody responses in an individual. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has prompted a wider application of this technology to meet the public health challenge of pandemic threats in the modern era. Herein, a combinatorial human antibody library constructed 20 years before the coronavirus disease 2019 (COVID-19) pandemic is used to discover three highly potent antibodies that selectively bind SARS-CoV-2 spike protein and neutralize authentic SARS-CoV-2 virus. Compared to neutralizing antibodies from COVID-19 patients with generally low somatic hypermutation (SHM), these three antibodies contain over 13-22 SHMs, many of which are involved in specific interactions in their crystal structures with SARS-CoV-2 spike receptor binding domain. The identification of these somatically mutated antibodies in a pre-pandemic library raises intriguing questions about the origin and evolution of these antibodies with respect to their reactivity with SARS-CoV-2.
		+
		+	Neutralizing Antibodies to SARS-CoV-2 Selected from a Human Antibody Library Constructed Decades Ago.,Qiang M, Ma P, Li Y, Liu H, Harding A, Min C, Wang F, Liu L, Yuan M, Ji Q, Tao P, Shi X, Li Z, Li T, Wang X, Zhang Y, Wu NC, Lee CD, Zhu X, Gilbert-Jaramillo J, Zhang C, Saxena A, Huang X, Wang H, James W, Dwek RA, Wilson IA, Yang G, Lerner RA Adv Sci (Weinh). 2022 Jan;9(1):e2102181. doi: 10.1002/advs.202102181. Epub 2021 , Oct 29. PMID:34716683<ref>PMID:34716683</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7kn3" 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: Liu H]]
		+	[[Category: Wilson IA]]
		+	[[Category: Zhu X]]

OCA at 06:50, 22 September 2021

OCA — Wed, 22 Sep 2021 06:50:46 GMT

←Older revision		Revision as of 06:50, 22 September 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7kn3 ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7kn3' size='340' side='right'caption='[[7kn3]]' 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=7kn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kn3 OCA], [https://pdbe.org/7kn3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kn3 RCSB], [https://www.ebi.ac.uk/pdbsum/7kn3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kn3 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 05:13, 9 December 2020

OCA — Wed, 09 Dec 2020 05:13:33 GMT

←Older revision		Revision as of 05:13, 9 December 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7kn3 is ON HOLD	+	The entry 7kn3 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7kn3" [edit=sysop:move=sysop]

OCA — Wed, 11 Nov 2020 06:35:54 GMT

Protected "7kn3" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:35, 11 November 2020

OCA: New page: '''Unreleased structure''' The entry 7kn3 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 11 Nov 2020 06:35:53 GMT

New page: '''Unreleased structure''' The entry 7kn3 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7kn3 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7kn3 - Revision history

OCA at 15:28, 18 October 2023

OCA at 06:50, 22 September 2021

OCA at 05:13, 9 December 2020

OCA: Protected "7kn3" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7kn3 is ON HOLD Authors: Description: Category: Unreleased Structures