OCA at 19:32, 19 October 2022

OCA — Wed, 19 Oct 2022 19:32:53 GMT

←Older revision		Revision as of 19:32, 19 October 2022
Line 1:		Line 1:

-	====	+	==Local refinement of cryo-EM structure of the interface of the Omicron RBD in complex with antibodies B-182.1 and A19-46.1==
-	<StructureSection load='7u0d' size='340' side='right'caption='[[7u0d]]' scene=''>	+	<StructureSection load='7u0d' size='340' side='right'caption='[[7u0d]], [[Resolution\|resolution]] 4.80Å' 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'>[[7u0d]] is a 5 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=7U0D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7U0D 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=7u0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u0d OCA], [https://pdbe.org/7u0d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u0d RCSB], [https://www.ebi.ac.uk/pdbsum/7u0d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u0d ProSAT]</span></td></tr>	+	</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=7u0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u0d OCA], [https://pdbe.org/7u0d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u0d RCSB], [https://www.ebi.ac.uk/pdbsum/7u0d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u0d 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 rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 (Omicron) variant and its resistance to neutralization by vaccinee and convalescent sera are driving a search for monoclonal antibodies with potent neutralization. To provide insight into effective neutralization, we determined cryo-electron microscopy structures and evaluated receptor binding domain (RBD) antibodies for their ability to bind and neutralize B.1.1.529. Mutations altered 16% of the B.1.1.529 RBD surface, clustered on an RBD ridge overlapping the angiotensin-converting enzyme 2 (ACE2)-binding surface and reduced binding of most antibodies. Substantial inhibitory activity was retained by select monoclonal antibodies-including A23-58.1, B1-182.1, COV2-2196, S2E12, A19-46.1, S309, and LY-CoV1404-that accommodated these changes and neutralized B.1.1.529. We identified combinations of antibodies with synergistic neutralization. The analysis revealed structural mechanisms for maintenance of potent neutralization against emerging variants.
		+
		+	Structural basis for potent antibody neutralization of SARS-CoV-2 variants including B.1.1.529.,Zhou T, Wang L, Misasi J, Pegu A, Zhang Y, Harris DR, Olia AS, Talana CA, Yang ES, Chen M, Choe M, Shi W, Teng IT, Creanga A, Jenkins C, Leung K, Liu T, Stancofski ED, Stephens T, Zhang B, Tsybovsky Y, Graham BS, Mascola JR, Sullivan NJ, Kwong PD Science. 2022 Apr 22;376(6591):eabn8897. doi: 10.1126/science.abn8897. Epub 2022 , Apr 22. PMID:35324257<ref>PMID:35324257</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7u0d" 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: Zhou T]]
		+	[[Category: Kwong PD]]

OCA at 10:48, 30 March 2022

OCA — Wed, 30 Mar 2022 10:48:21 GMT

←Older revision		Revision as of 10:48, 30 March 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7u0d ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7u0d' size='340' side='right'caption='[[7u0d]]' 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=7u0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u0d OCA], [https://pdbe.org/7u0d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u0d RCSB], [https://www.ebi.ac.uk/pdbsum/7u0d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u0d ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 05:05, 2 March 2022

OCA — Wed, 02 Mar 2022 05:05:57 GMT

←Older revision		Revision as of 05:05, 2 March 2022
Line 3:		Line 3:
	The entry 7u0d is ON HOLD		The entry 7u0d is ON HOLD

-	Authors: ~~Zhou, T., kwong, P.D.~~	+	Authors:

-	Description: ~~Local refinement of cryo-EM structure of the interface of the Omicron RBD in complex with antibodies B-182.1 and A19-46.1~~	+	Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Kwong, P.D]]
-	[[Category: Zhou, T]]

OCA: Protected "7u0d" [edit=sysop:move=sysop]

OCA — Wed, 23 Feb 2022 06:36:11 GMT

Protected "7u0d" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:36, 23 February 2022

OCA: New page: '''Unreleased structure''' The entry 7u0d is ON HOLD Authors: Zhou, T., kwong, P.D. Description: Local refinement of cryo-EM structure of the interface of the Omicron RBD in complex wi...

OCA — Wed, 23 Feb 2022 06:36:10 GMT

New page: '''Unreleased structure''' The entry 7u0d is ON HOLD Authors: Zhou, T., kwong, P.D. Description: Local refinement of cryo-EM structure of the interface of the Omicron RBD in complex wi...

New page

'''Unreleased structure'''

The entry 7u0d is ON HOLD

Authors: Zhou, T., kwong, P.D.

Description: Local refinement of cryo-EM structure of the interface of the Omicron RBD in complex with antibodies B-182.1 and A19-46.1
[[Category: Unreleased Structures]]
[[Category: Kwong, P.D]]
[[Category: Zhou, T]]

7u0d - Revision history

OCA at 19:32, 19 October 2022

OCA at 10:48, 30 March 2022

OCA at 05:05, 2 March 2022

OCA: Protected "7u0d" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7u0d is ON HOLD Authors: Zhou, T., kwong, P.D. Description: Local refinement of cryo-EM structure of the interface of the Omicron RBD in complex wi...