OCA at 15:19, 18 October 2023

OCA — Wed, 18 Oct 2023 15:19:39 GMT

←Older revision		Revision as of 15:19, 18 October 2023
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-	====	+	==Structure of the SARS-CoV-2 receptor binding domain in complex with the human neutralizing antibody Fab fragment, C102==
-	<StructureSection load='7k8m' size='340' side='right'caption='[[7k8m]]' scene=''>	+	<StructureSection load='7k8m' size='340' side='right'caption='[[7k8m]], [[Resolution\|resolution]] 3.20Å' 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 [~~http~~://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7k8m]] 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=7K8M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7K8M FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=7k8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k8m OCA], [~~http~~://pdbe.org/7k8m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7k8m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7k8m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7k8m 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]] 3.2Å</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=7k8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k8m OCA], [https://pdbe.org/7k8m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7k8m RCSB], [https://www.ebi.ac.uk/pdbsum/7k8m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7k8m 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 ==
		+	The COVID-19 pandemic presents an urgent health crisis. Human neutralizing antibodies (hNAbs) that target the host ACE2 receptor-binding domain (RBD) of the SARS-CoV-2 spike(1-5) show therapeutic promise and are being evaluated clincally(6-8). To determine structural correlates of SARS-CoV-2 neutralization, we solved 8 new structures of distinct COVID-19 hNAbs(5) in complex with SARS-CoV-2 spike trimer or RBD. Structural comparisons allowed classification into categories: (1) VH3-53 hNAbs with short CDRH3s that block ACE2 and bind only to "up" RBDs, (2) ACE2-blocking hNAbs that bind both "up" and "down" RBDs and can contact adjacent RBDs, (3) hNAbs that bind outside the ACE2 site and recognize "up" and "down" RBDs, and (4) Previously-described antibodies that do not block ACE2 and bind only "up" RBDs(9). Class 2 comprised four hNAbs whose epitopes bridged RBDs, including a VH3-53 hNAb that used a long CDRH3 with a hydrophobic tip to bridge between adjacent "down" RBDs, thereby locking the spike into a closed conformation. Epitope/paratope mapping revealed few interactions with host-derived N-glycans and minor contributions of antibody somatic hypermutations to epitope contacts. Affinity measurements and mapping of naturally-occurring and in vitro-selected spike mutants in 3D provided insight into the potential for SARS-CoV-2 escape from antibodies elicited during infection or delivered therapeutically. These classifications and structural analyses provide rules for assigning current and future human RBD-targeting antibodies into classes, evaluating avidity effects, suggesting combinations for clinical use, and providing insight into immune responses against SARS-CoV-2.
		+
		+	SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies.,Barnes CO, Jette CA, Abernathy ME, Dam KA, Esswein SR, Gristick HB, Malyutin AG, Sharaf NG, Huey-Tubman KE, Lee YE, Robbiani DF, Nussenzweig MC, West AP Jr, Bjorkman PJ Nature. 2020 Oct 12. pii: 10.1038/s41586-020-2852-1. doi:, 10.1038/s41586-020-2852-1. PMID:33045718<ref>PMID:33045718</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7k8m" 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: Barnes CO]]
		+	[[Category: Bjorkman PJ]]
		+	[[Category: Jette CA]]

OCA at 08:18, 21 October 2020

OCA — Wed, 21 Oct 2020 08:18:13 GMT

←Older revision		Revision as of 08:18, 21 October 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 7k8m ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7k8m' size='340' side='right'caption='[[7k8m]]' scene=''>
-	~~Authors~~: ~~Jette, C~~.A.~~, Barnes, C~~.O.~~, Bjorkman, P~~.J.	+	== 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 [http://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of an anti-SARS~~-~~CoV-2 human neutralizing antibody Fab fragment~~, ~~C110~~	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7k8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k8m OCA], [http://pdbe.org/7k8m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7k8m RCSB], [http://www.ebi.ac.uk/pdbsum/7k8m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7k8m ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: ~~Barnes~~, C.O]]	+	__TOC__
-	[[Category: ~~Bjorkman, P.J~~]]	+	</StructureSection>
-	[[Category: ~~Jette, C.A~~]]	+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA: Protected "7k8m" [edit=sysop:move=sysop]

OCA — Wed, 07 Oct 2020 04:45:50 GMT

Protected "7k8m" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:45, 7 October 2020

OCA: New page: '''Unreleased structure''' The entry 7k8m is ON HOLD Authors: Jette, C.A., Barnes, C.O., Bjorkman, P.J. Description: Crystal structure of an anti-SARS-CoV-2 human neutralizing antibody...

OCA — Wed, 07 Oct 2020 04:45:49 GMT

New page: '''Unreleased structure''' The entry 7k8m is ON HOLD Authors: Jette, C.A., Barnes, C.O., Bjorkman, P.J. Description: Crystal structure of an anti-SARS-CoV-2 human neutralizing antibody...

New page

'''Unreleased structure'''

The entry 7k8m is ON HOLD

Authors: Jette, C.A., Barnes, C.O., Bjorkman, P.J.

Description: Crystal structure of an anti-SARS-CoV-2 human neutralizing antibody Fab fragment, C110
[[Category: Unreleased Structures]]
[[Category: Barnes, C.O]]
[[Category: Bjorkman, P.J]]
[[Category: Jette, C.A]]

7k8m - Revision history

OCA at 15:19, 18 October 2023

OCA at 08:18, 21 October 2020

OCA: Protected "7k8m" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7k8m is ON HOLD Authors: Jette, C.A., Barnes, C.O., Bjorkman, P.J. Description: Crystal structure of an anti-SARS-CoV-2 human neutralizing antibody...