OCA at 12:33, 1 February 2024

OCA — Thu, 01 Feb 2024 12:33:52 GMT

←Older revision		Revision as of 12:33, 1 February 2024
Line 1:		Line 1:

-	====	+	==Crystal structure of the N501Y mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-269 Fab==
-	<StructureSection load='7neg' size='340' side='right'caption='[[7neg]]' scene=''>	+	<StructureSection load='7neg' size='340' side='right'caption='[[7neg]], [[Resolution\|resolution]] 2.19Å' 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'>[[7neg]] 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=7NEG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NEG 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=7neg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7neg OCA], [https://pdbe.org/7neg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7neg RCSB], [https://www.ebi.ac.uk/pdbsum/7neg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7neg 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]] 2.19Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=7neg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7neg OCA], [https://pdbe.org/7neg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7neg RCSB], [https://www.ebi.ac.uk/pdbsum/7neg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7neg 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 ==
		+	SARS-CoV-2 has caused over 2 million deaths in little over a year. Vaccines are being deployed at scale, aiming to generate responses against the virus spike. The scale of the pandemic and error-prone virus replication is leading to the appearance of mutant viruses and potentially escape from antibody responses. Variant B.1.1.7, now dominant in the UK, with increased transmission, harbors 9 amino acid changes in the spike, including N501Y in the ACE2 interacting surface. We examine the ability of B.1.1.7 to evade antibody responses elicited by natural SARS-CoV-2 infection or vaccination. We map the impact of N501Y by structure/function analysis of a large panel of well-characterized monoclonal antibodies. B.1.1.7 is harder to neutralize than parental virus, compromising neutralization by some members of a major class of public antibodies through light-chain contacts with residue 501. However, widespread escape from monoclonal antibodies or antibody responses generated by natural infection or vaccination was not observed.
		+
		+	Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera.,Supasa P, Zhou D, Dejnirattisai W, Liu C, Mentzer AJ, Ginn HM, Zhao Y, Duyvesteyn HME, Nutalai R, Tuekprakhon A, Wang B, Paesen GC, Slon-Campos J, Lopez-Camacho C, Hallis B, Coombes N, Bewley KR, Charlton S, Walter TS, Barnes E, Dunachie SJ, Skelly D, Lumley SF, Baker N, Shaik I, Humphries HE, Godwin K, Gent N, Sienkiewicz A, Dold C, Levin R, Dong T, Pollard AJ, Knight JC, Klenerman P, Crook D, Lambe T, Clutterbuck E, Bibi S, Flaxman A, Bittaye M, Belij-Rammerstorfer S, Gilbert S, Hall DR, Williams MA, Paterson NG, James W, Carroll MW, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR Cell. 2021 Apr 15;184(8):2201-2211.e7. doi: 10.1016/j.cell.2021.02.033. Epub 2021 , Feb 18. PMID:33743891<ref>PMID:33743891</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7neg" 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: Ren J]]
		+	[[Category: Stuart D]]
		+	[[Category: Zhou D]]

OCA at 14:47, 3 March 2021

OCA — Wed, 03 Mar 2021 14:47:44 GMT

←Older revision		Revision as of 14:47, 3 March 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7neg ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7neg' size='340' side='right'caption='[[7neg]]' scene=''>
-	~~Authors~~: ~~Zhou, D~~.~~, Ren, J~~.~~, Stuart, D~~.	+	== 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: Crystal structure of the N501Y mutant receptor binding domain of SARS-CoV~~-~~2 Spike glycoprotein in complex with COVOX-269 Fab~~	+	</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=7neg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7neg OCA], [https://pdbe.org/7neg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7neg RCSB], [https://www.ebi.ac.uk/pdbsum/7neg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7neg ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Ren, J~~]]	+	__TOC__
-	[[Category: ~~Stuart, D~~]]	+	</StructureSection>
-	[[Category: ~~Zhou, D~~]]	+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 08:52, 17 February 2021

OCA — Wed, 17 Feb 2021 08:52:31 GMT

←Older revision		Revision as of 08:52, 17 February 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Zhou, D., Ren, J., Stuart, D.		Authors: Zhou, D., Ren, J., Stuart, D.

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

OCA — Wed, 10 Feb 2021 09:27:09 GMT

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

←Older revision

Revision as of 09:27, 10 February 2021

OCA: New page: '''Unreleased structure''' The entry 7neg is ON HOLD Authors: Zhou, D., Ren, J., Stuart, D. Description: Crystal structure of the N501Y mutant receptor binding domain of SARS-CoV-2 Spi...

OCA — Wed, 10 Feb 2021 09:27:08 GMT

New page: '''Unreleased structure''' The entry 7neg is ON HOLD Authors: Zhou, D., Ren, J., Stuart, D. Description: Crystal structure of the N501Y mutant receptor binding domain of SARS-CoV-2 Spi...

New page

'''Unreleased structure'''

The entry 7neg is ON HOLD

Authors: Zhou, D., Ren, J., Stuart, D.

Description: Crystal structure of the N501Y mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-269 Fab
[[Category: Unreleased Structures]]
[[Category: Ren, J]]
[[Category: Stuart, D]]
[[Category: Zhou, D]]

7neg - Revision history

OCA at 12:33, 1 February 2024

OCA at 14:47, 3 March 2021

OCA at 08:52, 17 February 2021

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

OCA: New page: '''Unreleased structure''' The entry 7neg is ON HOLD Authors: Zhou, D., Ren, J., Stuart, D. Description: Crystal structure of the N501Y mutant receptor binding domain of SARS-CoV-2 Spi...