7tnw - Revision history

OCA at 14:52, 31 August 2022

OCA — Wed, 31 Aug 2022 14:52:17 GMT

←Older revision		Revision as of 14:52, 31 August 2022
Line 1:		Line 1:

	==Structural and functional impact by SARS-CoV-2 Omicron spike mutations==		==Structural and functional impact by SARS-CoV-2 Omicron spike mutations==
-	<StructureSection load='7tnw' size='340' side='right'caption='[[7tnw]]~~, [[Resolution\|resolution]] 3.10Å~~' scene=''>	+	<StructureSection load='7tnw' size='340' side='right'caption='[[7tnw]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[7tnw]] is a 3 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TNW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TNW FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TNW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TNW FirstGlance]. <br>
-	</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>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>	+	</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=7tnw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tnw OCA], [https://pdbe.org/7tnw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tnw RCSB], [https://www.ebi.ac.uk/pdbsum/7tnw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tnw 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=7tnw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tnw OCA], [https://pdbe.org/7tnw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tnw RCSB], [https://www.ebi.ac.uk/pdbsum/7tnw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tnw 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 Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), bearing an unusually high number of mutations, has become a dominant strain in many countries within several weeks. We report here structural, functional, and antigenic properties of its full-length spike (S) protein with a native sequence in comparison with those of previously prevalent variants. Omicron S requires a substantially higher level of host receptor ACE2 for efficient membrane fusion than other variants, possibly explaining its unexpected cellular tropism. Mutations not only remodel the antigenic structure of the N-terminal domain of the S protein but also alter the surface of the receptor-binding domain in a way not seen in other variants, consistent with its remarkable resistance to neutralizing antibodies. These results suggest that Omicron S has acquired an extraordinary ability to evade host immunity by excessive mutations, which also compromise its fusogenic capability.
-
-	Structural and functional impact by SARS-CoV-2 Omicron spike mutations.,Zhang J, Cai Y, Lavine CL, Peng H, Zhu H, Anand K, Tong P, Gautam A, Mayer ML, Rits-Volloch S, Wang S, Sliz P, Wesemann DR, Yang W, Seaman MS, Lu J, Xiao T, Chen B Cell Rep. 2022 Apr 26;39(4):110729. doi: 10.1016/j.celrep.2022.110729. Epub 2022 , Apr 11. PMID:35452593<ref>PMID:35452593</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7tnw" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cai~~, Y F~~]]	+	[[Category: Cai YF]]
-	[[Category: Chen, B]]	+	[[Category: Chen B]]
-	[[Category: Peng~~, H Q~~]]	+	[[Category: Peng HQ]]
-	[[Category: Volloch~~, S R~~]]	+	[[Category: Volloch SR]]
-	[[Category: Xiao~~, T S~~]]	+	[[Category: Xiao TS]]
-	[[Category: Zhang, J]]	+	[[Category: Zhang J]]
-	~~[[Category: Viral protein~~]]	+

OCA at 13:09, 4 May 2022

OCA — Wed, 04 May 2022 13:09:47 GMT

←Older revision		Revision as of 13:09, 4 May 2022
Line 1:		Line 1:

	==Structural and functional impact by SARS-CoV-2 Omicron spike mutations==		==Structural and functional impact by SARS-CoV-2 Omicron spike mutations==
-	<StructureSection load='7tnw' size='340' side='right'caption='[[7tnw]]' scene=''>	+	<StructureSection load='7tnw' size='340' side='right'caption='[[7tnw]], [[Resolution\|resolution]] 3.10Å' 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=7TNW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TNW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7tnw]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TNW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TNW 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=7tnw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tnw OCA], [https://pdbe.org/7tnw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tnw RCSB], [https://www.ebi.ac.uk/pdbsum/7tnw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tnw 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>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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=7tnw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tnw OCA], [https://pdbe.org/7tnw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tnw RCSB], [https://www.ebi.ac.uk/pdbsum/7tnw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tnw 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 Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), bearing an unusually high number of mutations, has become a dominant strain in many countries within several weeks. We report here structural, functional, and antigenic properties of its full-length spike (S) protein with a native sequence in comparison with those of previously prevalent variants. Omicron S requires a substantially higher level of host receptor ACE2 for efficient membrane fusion than other variants, possibly explaining its unexpected cellular tropism. Mutations not only remodel the antigenic structure of the N-terminal domain of the S protein but also alter the surface of the receptor-binding domain in a way not seen in other variants, consistent with its remarkable resistance to neutralizing antibodies. These results suggest that Omicron S has acquired an extraordinary ability to evade host immunity by excessive mutations, which also compromise its fusogenic capability.
		+
		+	Structural and functional impact by SARS-CoV-2 Omicron spike mutations.,Zhang J, Cai Y, Lavine CL, Peng H, Zhu H, Anand K, Tong P, Gautam A, Mayer ML, Rits-Volloch S, Wang S, Sliz P, Wesemann DR, Yang W, Seaman MS, Lu J, Xiao T, Chen B Cell Rep. 2022 Apr 26;39(4):110729. doi: 10.1016/j.celrep.2022.110729. Epub 2022 , Apr 11. PMID:35452593<ref>PMID:35452593</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7tnw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cai YF]]	+	[[Category: Cai, Y F]]
-	[[Category: Chen B]]	+	[[Category: Chen, B]]
-	[[Category: Peng HQ]]	+	[[Category: Peng, H Q]]
-	[[Category: Volloch SR]]	+	[[Category: Volloch, S R]]
-	[[Category: Xiao TS]]	+	[[Category: Xiao, T S]]
-	[[Category: Zhang J]]	+	[[Category: Zhang, J]]
		+	[[Category: Viral protein]]

OCA at 10:18, 16 February 2022

OCA — Wed, 16 Feb 2022 10:18:54 GMT

←Older revision		Revision as of 10:18, 16 February 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7tnw is ~~ON HOLD~~	+	==Structural and functional impact by SARS-CoV-2 Omicron spike mutations==
-		+	<StructureSection load='7tnw' size='340' side='right'caption='[[7tnw]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TNW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TNW 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=7tnw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tnw OCA], [https://pdbe.org/7tnw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tnw RCSB], [https://www.ebi.ac.uk/pdbsum/7tnw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tnw ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Cai YF]]
		+	[[Category: Chen B]]
		+	[[Category: Peng HQ]]
		+	[[Category: Volloch SR]]
		+	[[Category: Xiao TS]]
		+	[[Category: Zhang J]]

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

OCA — Wed, 02 Feb 2022 05:37:56 GMT

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

←Older revision

Revision as of 05:37, 2 February 2022

OCA: New page: '''Unreleased structure''' The entry 7tnw is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 02 Feb 2022 05:37:55 GMT

New page: '''Unreleased structure''' The entry 7tnw is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7tnw is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]