7q0h - Revision history

OCA at 13:11, 1 February 2024

2024-02-01T13:11:55Z

←Older revision		Revision as of 13:11, 1 February 2024
Line 1:		Line 1:

-	====	+	==Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-50 and Beta-54==
-	<StructureSection load='7q0h' size='340' side='right'caption='[[7q0h]]' scene=''>	+	<StructureSection load='7q0h' size='340' side='right'caption='[[7q0h]], [[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'>[[7q0h]] 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=7Q0H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Q0H 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=7q0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7q0h OCA], [https://pdbe.org/7q0h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7q0h RCSB], [https://www.ebi.ac.uk/pdbsum/7q0h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7q0h 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=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <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=7q0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7q0h OCA], [https://pdbe.org/7q0h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7q0h RCSB], [https://www.ebi.ac.uk/pdbsum/7q0h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7q0h 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 ==
		+	Alpha-B.1.1.7, Beta-B.1.351, Gamma-P.1, and Delta-B.1.617.2 variants of SARS-CoV-2 express multiple mutations in the spike protein (S). These may alter the antigenic structure of S, causing escape from natural or vaccine-induced immunity. Beta is particularly difficult to neutralize using serum induced by early pandemic SARS-CoV-2 strains and is most antigenically separated from Delta. To understand this, we generated 674 mAbs from Beta-infected individuals and performed a detailed structure-function analysis of the 27 most potent mAbs: one binding the spike N-terminal domain (NTD), the rest the receptor-binding domain (RBD). Two of these RBD-binding mAbs recognize a neutralizing epitope conserved between SARS-CoV-1 and -2, while 18 target mutated residues in Beta: K417N, E484K, and N501Y. There is a major response to N501Y, including a public IgVH4-39 sequence, with E484K and K417N also targeted. Recognition of these key residues underscores why serum from Beta cases poorly neutralizes early pandemic and Delta viruses.
		+
		+	The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.,Liu C, Zhou D, Nutalai R, Duyvesteyn HME, Tuekprakhon A, Ginn HM, Dejnirattisai W, Supasa P, Mentzer AJ, Wang B, Case JB, Zhao Y, Skelly DT, Chen RE, Johnson SA, Ritter TG, Mason C, Malik T, Temperton N, Paterson NG, Williams MA, Hall DR, Clare DK, Howe A, Goulder PJR, Fry EE, Diamond MS, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR Cell Host Microbe. 2022 Jan 12;30(1):53-68.e12. doi: 10.1016/j.chom.2021.11.013. , Epub 2021 Nov 27. PMID:34921776<ref>PMID:34921776</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7q0h" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[Spike protein 3D structures\|Spike protein 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 DI]]
		+	[[Category: Zhou D]]

OCA at 15:28, 22 December 2021

2021-12-22T15:28:28Z

←Older revision		Revision as of 15:28, 22 December 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7q0h ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7q0h' size='340' side='right'caption='[[7q0h]]' scene=''>
-	~~Authors~~: ~~Zhou, D~~.~~, Ren, J~~.~~, Stuart, D~~.I.	+	== 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 ~~receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-50 and Beta-54~~	+	</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=7q0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7q0h OCA], [https://pdbe.org/7q0h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7q0h RCSB], [https://www.ebi.ac.uk/pdbsum/7q0h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7q0h ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Ren~~, J]]	+	__TOC__
-	[[Category: ~~Stuart, D.I~~]]	+	</StructureSection>
-	[[Category: ~~Zhou, D~~]]	+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 10:47, 24 November 2021

2021-11-24T10:47:02Z

←Older revision		Revision as of 10:47, 24 November 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7q0h is ON HOLD	+	The entry 7q0h is ON HOLD until Paper Publication

	Authors: Zhou, D., Ren, J., Stuart, D.I.		Authors: Zhou, D., Ren, J., Stuart, D.I.
Line 7:		Line 7:
	Description: Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-50 and Beta-54		Description: Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-50 and Beta-54
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Zhou, D]]
	[[Category: Ren, J]]		[[Category: Ren, J]]
	[[Category: Stuart, D.I]]		[[Category: Stuart, D.I]]
		+	[[Category: Zhou, D]]

OCA: Protected "7q0h" [edit=sysop:move=sysop]

2021-10-20T15:02:17Z

Protected "7q0h" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:02, 20 October 2021

OCA: New page: '''Unreleased structure''' The entry 7q0h is ON HOLD Authors: Zhou, D., Ren, J., Stuart, D.I. Description: Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant s...

2021-10-20T15:02:16Z

New page: '''Unreleased structure''' The entry 7q0h is ON HOLD Authors: Zhou, D., Ren, J., Stuart, D.I. Description: Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant s...

New page

'''Unreleased structure'''

The entry 7q0h is ON HOLD

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

Description: Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-50 and Beta-54
[[Category: Unreleased Structures]]
[[Category: Zhou, D]]
[[Category: Ren, J]]
[[Category: Stuart, D.I]]