7qnw - Revision history

OCA at 13:20, 1 February 2024

OCA — Thu, 01 Feb 2024 13:20:18 GMT

←Older revision		Revision as of 13:20, 1 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7qnw]] 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=7QNW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QNW FirstGlance]. <br>		<table><tr><td colspan='2'>[[7qnw]] 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=7QNW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QNW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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]] 2.4Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=7qnw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qnw OCA], [https://pdbe.org/7qnw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qnw RCSB], [https://www.ebi.ac.uk/pdbsum/7qnw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qnw ProSAT]</span></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=7qnw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qnw OCA], [https://pdbe.org/7qnw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qnw RCSB], [https://www.ebi.ac.uk/pdbsum/7qnw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qnw ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:24, 26 October 2022

OCA — Wed, 26 Oct 2022 06:24:49 GMT

←Older revision		Revision as of 06:24, 26 October 2022
Line 1:		Line 1:

-	====	+	==The receptor binding domain of SARS-CoV-2 Omicron variant spike glycoprotein in complex with Beta-55 and EY6A Fabs==
-	<StructureSection load='7qnw' size='340' side='right'caption='[[7qnw]]' scene=''>	+	<StructureSection load='7qnw' size='340' side='right'caption='[[7qnw]], [[Resolution\|resolution]] 2.40Å' 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'>[[7qnw]] 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=7QNW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QNW 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=7qnw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qnw OCA], [https://pdbe.org/7qnw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qnw RCSB], [https://www.ebi.ac.uk/pdbsum/7qnw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qnw 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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=7qnw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qnw OCA], [https://pdbe.org/7qnw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qnw RCSB], [https://www.ebi.ac.uk/pdbsum/7qnw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qnw 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 ==
		+	On 24(th) November 2021, the sequence of a new SARS-CoV-2 viral isolate Omicron-B.1.1.529 was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titers of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic Alpha, Beta, Gamma, or Delta are substantially reduced, or the sera failed to neutralize. Titers against Omicron are boosted by third vaccine doses and are high in both vaccinated individuals and those infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of the large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses and uses mutations that confer tight binding to ACE2 to unleash evolution driven by immune escape. This leads to a large number of mutations in the ACE2 binding site and rebalances receptor affinity to that of earlier pandemic viruses.
		+
		+	SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses.,Dejnirattisai W, Huo J, Zhou D, Zahradnik J, Supasa P, Liu C, Duyvesteyn HME, Ginn HM, Mentzer AJ, Tuekprakhon A, Nutalai R, Wang B, Dijokaite A, Khan S, Avinoam O, Bahar M, Skelly D, Adele S, Johnson SA, Amini A, Ritter TG, Mason C, Dold C, Pan D, Assadi S, Bellass A, Omo-Dare N, Koeckerling D, Flaxman A, Jenkin D, Aley PK, Voysey M, Costa Clemens SA, Naveca FG, Nascimento V, Nascimento F, Fernandes da Costa C, Resende PC, Pauvolid-Correa A, Siqueira MM, Baillie V, Serafin N, Kwatra G, Da Silva K, Madhi SA, Nunes MC, Malik T, Openshaw PJM, Baillie JK, Semple MG, Townsend AR, Huang KA, Tan TK, Carroll MW, Klenerman P, Barnes E, Dunachie SJ, Constantinides B, Webster H, Crook D, Pollard AJ, Lambe T, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Schreiber G, Stuart DI, Screaton GR Cell. 2022 Feb 3;185(3):467-484.e15. doi: 10.1016/j.cell.2021.12.046. Epub 2022, Jan 4. PMID:35081335<ref>PMID:35081335</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7qnw" 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 DI]]
		+	[[Category: Zhou D]]

OCA at 07:30, 19 January 2022

OCA — Wed, 19 Jan 2022 07:30:46 GMT

←Older revision		Revision as of 07:30, 19 January 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7qnw ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7qnw' size='340' side='right'caption='[[7qnw]]' 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~~: ~~The receptor binding domain of SARS-CoV-2 Omicron variant spike glycoprotein in complex with Beta-55 and EY6A Fabs~~	+	</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=7qnw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qnw OCA], [https://pdbe.org/7qnw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qnw RCSB], [https://www.ebi.ac.uk/pdbsum/7qnw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qnw 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: Protected "7qnw" [edit=sysop:move=sysop]

OCA — Wed, 29 Dec 2021 11:57:26 GMT

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

←Older revision

Revision as of 11:57, 29 December 2021

OCA: New page: '''Unreleased structure''' The entry 7qnw is ON HOLD Authors: Zhou, D., Ren, J., Stuart, D.I. Description: The receptor binding domain of SARS-CoV-2 Omicron variant spike glycoprotein ...

OCA — Wed, 29 Dec 2021 11:57:25 GMT

New page: '''Unreleased structure''' The entry 7qnw is ON HOLD Authors: Zhou, D., Ren, J., Stuart, D.I. Description: The receptor binding domain of SARS-CoV-2 Omicron variant spike glycoprotein ...

New page

'''Unreleased structure'''

The entry 7qnw is ON HOLD

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

Description: The receptor binding domain of SARS-CoV-2 Omicron variant spike glycoprotein in complex with Beta-55 and EY6A Fabs
[[Category: Unreleased Structures]]
[[Category: Ren, J]]
[[Category: Stuart, D.I]]
[[Category: Zhou, D]]