OCA at 15:38, 18 October 2023

OCA — Wed, 18 Oct 2023 15:38:03 GMT

←Older revision		Revision as of 15:38, 18 October 2023
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-	====	+	==Crystallographic structure of neutralizing antibody 2-15 in complex with SARS-CoV-2 spike receptor-binding Domain (RBD).==
-	<StructureSection load='7l5b' size='340' side='right'caption='[[7l5b]]' scene=''>	+	<StructureSection load='7l5b' size='340' side='right'caption='[[7l5b]], [[Resolution\|resolution]] 3.18Å' 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'>[[7l5b]] is a 3 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=7L5B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7L5B 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=7l5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l5b OCA], [https://pdbe.org/7l5b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l5b RCSB], [https://www.ebi.ac.uk/pdbsum/7l5b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l5b 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]] 3.18Å</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=7l5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l5b OCA], [https://pdbe.org/7l5b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l5b RCSB], [https://www.ebi.ac.uk/pdbsum/7l5b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l5b 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 ==
		+	Antibodies with heavy chains that derive from the VH1-2 gene constitute some of the most potent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-neutralizing antibodies yet identified. To provide insight into whether these genetic similarities inform common modes of recognition, we determine the structures of the SARS-CoV-2 spike in complex with three VH1-2-derived antibodies: 2-15, 2-43, and H4. All three use VH1-2-encoded motifs to recognize the receptor-binding domain (RBD), with heavy-chain N53I-enhancing binding and light-chain tyrosines recognizing F486(RBD). Despite these similarities, class members bind both RBD-up and -down conformations of the spike, with a subset of antibodies using elongated CDRH3s to recognize glycan N343 on a neighboring RBD-a quaternary interaction accommodated by an increase in RBD separation of up to 12 A. The VH1-2 antibody class, thus, uses modular recognition encoded by modular genetic elements to effect potent neutralization, with the VH-gene component specifying recognition of RBD and the CDRH3 component specifying quaternary interactions.
		+
		+	Modular basis for potent SARS-CoV-2 neutralization by a prevalent VH1-2-derived antibody class.,Rapp M, Guo Y, Reddem ER, Yu J, Liu L, Wang P, Cerutti G, Katsamba P, Bimela JS, Bahna FA, Mannepalli SM, Zhang B, Kwong PD, Huang Y, Ho DD, Shapiro L, Sheng Z Cell Rep. 2021 Apr 6;35(1):108950. doi: 10.1016/j.celrep.2021.108950. Epub 2021 , Mar 19. PMID:33794145<ref>PMID:33794145</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7l5b" 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: Reddem ER]]
		+	[[Category: Shapiro L]]

OCA at 11:04, 10 February 2021

OCA — Wed, 10 Feb 2021 11:04:41 GMT

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

-	~~The entry~~ 7l5b ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7l5b' size='340' side='right'caption='[[7l5b]]' 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=7l5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l5b OCA], [https://pdbe.org/7l5b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l5b RCSB], [https://www.ebi.ac.uk/pdbsum/7l5b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l5b ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 06:44, 27 January 2021

OCA — Wed, 27 Jan 2021 06:44:37 GMT

←Older revision		Revision as of 06:44, 27 January 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7l5b is ON HOLD	+	The entry 7l5b is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7l5b" [edit=sysop:move=sysop]

OCA — Wed, 30 Dec 2020 05:31:19 GMT

Protected "7l5b" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:31, 30 December 2020

OCA: New page: '''Unreleased structure''' The entry 7l5b is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 30 Dec 2020 05:31:18 GMT

New page: '''Unreleased structure''' The entry 7l5b is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7l5b is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7l5b - Revision history

OCA at 15:38, 18 October 2023

OCA at 11:04, 10 February 2021

OCA at 06:44, 27 January 2021

OCA: Protected "7l5b" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7l5b is ON HOLD Authors: Description: Category: Unreleased Structures