8qrf - Revision history

OCA at 05:58, 5 June 2024

2024-06-05T05:58:17Z

← Older revision		Revision as of 05:58, 5 June 2024
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	== Function ==		== 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]		[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 ==
			BA.2.86, a recently described sublineage of SARS-CoV-2 Omicron, contains many mutations in the spike gene. It appears to have originated from BA.2 and is distinct from the XBB variants responsible for many infections in 2023. The global spread and plethora of mutations in BA.2.86 has caused concern that it may possess greater immune-evasive potential, leading to a new wave of infection. Here, we examine the ability of BA.2.86 to evade the antibody response to infection using a panel of vaccinated or naturally infected sera and find that it shows marginally less immune evasion than XBB.1.5. We locate BA.2.86 in the antigenic landscape of recent variants and look at its ability to escape panels of potent monoclonal antibodies generated against contemporary SARS-CoV-2 infections. We demonstrate, and provide a structural explanation for, increased affinity of BA.2.86 to ACE2, which may increase transmissibility.

			A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity.,Liu C, Zhou D, Dijokaite-Guraliuc A, Supasa P, Duyvesteyn HME, Ginn HM, Selvaraj M, Mentzer AJ, Das R, de Silva TI, Ritter TG, Plowright M, Newman TAH, Stafford L, Kronsteiner B, Temperton N, Lui Y, Fellermeyer M, Goulder P, Klenerman P, Dunachie SJ, Barton MI, Kutuzov MA, Dushek O, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR Cell Rep Med. 2024 May 21;5(5):101553. doi: 10.1016/j.xcrm.2024.101553. Epub 2024 , May 8. PMID:38723626<ref>PMID:38723626</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 8qrf" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:33, 9 May 2024

2024-05-09T08:33:38Z

← Older revision		Revision as of 08:33, 9 May 2024
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	~~'''Unreleased structure'''~~

	~~The entry~~ 8qrf is ~~ON HOLD until Paper Publication~~		==SARS-CoV-2 delta RBD complexed with XBB-6 and beta-49 Fabs==
			<StructureSection load='8qrf' size='340' side='right'caption='[[8qrf]], [[Resolution\|resolution]] 3.70Å' scene=''>
	~~Authors~~: ~~Zhou~~, D., ~~Ren~~, J., ~~Stuart~~, D.I.		== Structural highlights ==
			<table><tr><td colspan='2'>[[8qrf]] 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=8QRF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8QRF FirstGlance]. <br>
	~~Description~~: ~~SARS~~-~~CoV~~-~~2 delta RBD complexed with XBB~~-6 and ~~beta~~-~~49 Fabs~~		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.7Å</td></tr>
	[[Category: ~~Unreleased~~ Structures]]		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	[[Category: Ren, J]]		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8qrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8qrf OCA], [https://pdbe.org/8qrf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8qrf RCSB], [https://www.ebi.ac.uk/pdbsum/8qrf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8qrf ProSAT]</span></td></tr>
	[[Category: Stuart~~, D.I~~]]		</table>
	[[Category: Zhou, D]]		== 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]
			== References ==
			<references/>
			__TOC__
			</StructureSection>
			[[Category: Homo sapiens]]
			[[Category: Large Structures]]
			[[Category: Severe acute respiratory syndrome coronavirus 2]]
			[[Category: Ren J]]
			[[Category: Stuart DI]]
			[[Category: Zhou D]]

OCA at 06:21, 29 November 2023

2023-11-29T06:21:30Z

← Older revision		Revision as of 06:21, 29 November 2023
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 8qrf is ON HOLD		The entry 8qrf is ON HOLD until Paper Publication

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

OCA at 05:49, 22 November 2023

2023-11-22T05:49:52Z

← Older revision		Revision as of 05:49, 22 November 2023
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 8qrf is ON HOLD ~~until Paper Publication~~		The entry 8qrf is ON HOLD

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

OCA at 05:17, 15 November 2023

2023-11-15T05:17:39Z

← Older revision		Revision as of 05:17, 15 November 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 8qrf is ON HOLD		The entry 8qrf is ON HOLD until Paper Publication

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

OCA: Protected "8qrf" [edit=sysop:move=sysop]

2023-10-18T12:12:05Z

Protected "8qrf" [edit=sysop:move=sysop]

← Older revision	Revision as of 12:12, 18 October 2023
(No difference)

OCA: New page: '''Unreleased structure''' The entry 8qrf is ON HOLD Authors: Zhou, D., Ren, J., Stuart, D.I. Description: SARS-CoV-2 delta RBD complexed with XBB-6 and beta-49 Fabs [[Category: Unrele...

2023-10-18T12:12:04Z

New page: '''Unreleased structure''' The entry 8qrf is ON HOLD Authors: Zhou, D., Ren, J., Stuart, D.I. Description: SARS-CoV-2 delta RBD complexed with XBB-6 and beta-49 Fabs [[Category: Unrele...

New page

'''Unreleased structure'''

The entry 8qrf is ON HOLD

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

Description: SARS-CoV-2 delta RBD complexed with XBB-6 and beta-49 Fabs
[[Category: Unreleased Structures]]
[[Category: Ren, J]]
[[Category: Stuart, D.I]]
[[Category: Zhou, D]]