OCA at 15:36, 18 October 2023

OCA — Wed, 18 Oct 2023 15:36:25 GMT

←Older revision		Revision as of 15:36, 18 October 2023
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-	====	+	==Crystallographic structure of neutralizing antibody 2-51 in complex with SARS-CoV-2 spike N-terminal domain (NTD)==
-	<StructureSection load='7l2c' size='340' side='right'caption='[[7l2c]]' scene=''>	+	<StructureSection load='7l2c' size='340' side='right'caption='[[7l2c]], [[Resolution\|resolution]] 3.65Å' 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'>[[7l2c]] 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=7L2C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7L2C 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=7l2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l2c OCA], [https://pdbe.org/7l2c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l2c RCSB], [https://www.ebi.ac.uk/pdbsum/7l2c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l2c 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]] 3.65Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=7l2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l2c OCA], [https://pdbe.org/7l2c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l2c RCSB], [https://www.ebi.ac.uk/pdbsum/7l2c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l2c 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 ==
		+	Numerous antibodies that neutralize SARS-CoV-2 have been identified, and these generally target either the receptor-binding domain (RBD) or the N-terminal domain (NTD) of the viral spike. While RBD-directed antibodies have been extensively studied, far less is known about NTD-directed antibodies. Here, we report cryo-EM and crystal structures for seven potent NTD-directed neutralizing antibodies in complex with spike or isolated NTD. These structures defined several antibody classes, with at least one observed in multiple convalescent donors. The structures revealed that all seven antibodies target a common surface, bordered by glycans N17, N74, N122, and N149. This site-formed primarily by a mobile beta-hairpin and several flexible loops-was highly electropositive, located at the periphery of the spike, and the largest glycan-free surface of NTD facing away from the viral membrane. Thus, in contrast to neutralizing RBD-directed antibodies that recognize multiple non-overlapping epitopes, potent NTD-directed neutralizing antibodies appear to target a single supersite.
		+
		+	Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite.,Cerutti G, Guo Y, Zhou T, Gorman J, Lee M, Rapp M, Reddem ER, Yu J, Bahna F, Bimela J, Huang Y, Katsamba PS, Liu L, Nair MS, Rawi R, Olia AS, Wang P, Zhang B, Chuang GY, Ho DD, Sheng Z, Kwong PD, Shapiro L Cell Host Microbe. 2021 May 12;29(5):819-833.e7. doi: 10.1016/j.chom.2021.03.005. , Epub 2021 Mar 12. PMID:33789084<ref>PMID:33789084</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7l2c" 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: Reddem ER]]
		+	[[Category: Shapiro L]]

OCA at 11:04, 10 February 2021

OCA — Wed, 10 Feb 2021 11:04:37 GMT

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

-	~~The entry~~ 7l2c ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7l2c' size='340' side='right'caption='[[7l2c]]' 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=7l2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l2c OCA], [https://pdbe.org/7l2c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l2c RCSB], [https://www.ebi.ac.uk/pdbsum/7l2c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l2c ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 06:52, 20 January 2021

OCA — Wed, 20 Jan 2021 06:52:06 GMT

←Older revision		Revision as of 06:52, 20 January 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7l2c is ON HOLD	+	The entry 7l2c is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7l2c" [edit=sysop:move=sysop]

OCA — Thu, 24 Dec 2020 08:11:28 GMT

Protected "7l2c" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:11, 24 December 2020

OCA: New page: '''Unreleased structure''' The entry 7l2c is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 24 Dec 2020 08:11:26 GMT

New page: '''Unreleased structure''' The entry 7l2c is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7l2c is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7l2c - Revision history

OCA at 15:36, 18 October 2023

OCA at 11:04, 10 February 2021

OCA at 06:52, 20 January 2021

OCA: Protected "7l2c" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7l2c is ON HOLD Authors: Description: Category: Unreleased Structures