7xo7 - Revision history

OCA at 14:13, 6 November 2024

2024-11-06T14:13:33Z

← Older revision		Revision as of 14:13, 6 November 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7xo7]] 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=7XO7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XO7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7xo7]] 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=7XO7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XO7 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.38Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7xo7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xo7 OCA], [https://pdbe.org/7xo7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xo7 RCSB], [https://www.ebi.ac.uk/pdbsum/7xo7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xo7 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=7xo7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xo7 OCA], [https://pdbe.org/7xo7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xo7 RCSB], [https://www.ebi.ac.uk/pdbsum/7xo7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xo7 ProSAT]</span></td></tr>
	</table>		</table>
	== 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 ==
			The Omicron BA.2 variant has become a dominant infective strain worldwide. Receptor binding studies show that the Omicron BA.2 spike trimer exhibits 11-fold and 2-fold higher potency in binding to human ACE2 than the spike trimer from the wildtype (WT) and Omicron BA.1 strains. The structure of the BA.2 spike trimer complexed with human ACE2 reveals that all three receptor-binding domains (RBDs) in the spike trimer are in open conformation, ready for ACE2 binding, thus providing a basis for the increased infectivity of the BA.2 strain. JMB2002, a therapeutic antibody that was shown to efficiently inhibit Omicron BA.1, also shows potent neutralization activities against Omicron BA.2. In addition, both BA.1 and BA.2 spike trimers are able to bind to mouse ACE2 with high potency. In contrast, the WT spike trimer binds well to cat ACE2 but not to mouse ACE2. The structures of both BA.1 and BA.2 spike trimer bound to mouse ACE2 reveal the basis for their high affinity interactions. Together, these results suggest a possible evolution pathway for Omicron BA.1 and BA.2 variants via a human-cat-mouse-human circle, which could have important implications in establishing an effective strategy for combating SARS-CoV-2 viral infections.

			Structural and biochemical mechanism for increased infectivity and immune evasion of Omicron BA.2 variant compared to BA.1 and their possible mouse origins.,Xu Y, Wu C, Cao X, Gu C, Liu H, Jiang M, Wang X, Yuan Q, Wu K, Liu J, Wang D, He X, Wang X, Deng SJ, Xu HE, Yin W Cell Res. 2022 Jul;32(7):609-620. doi: 10.1038/s41422-022-00672-4. Epub 2022 May , 31. PMID:35641567<ref>PMID:35641567</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7xo7" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Angiotensin-Converting Enzyme 3D structures\|Angiotensin-Converting Enzyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:29, 8 September 2022

2022-09-08T06:29:36Z

← Older revision		Revision as of 06:29, 8 September 2022
Line 1:		Line 1:

	====		==SARS-CoV-2 Omicron BA.2 Variant Spike Trimer with two human ACE2 Bound==
	<StructureSection load='7xo7' size='340' side='right'caption='[[7xo7]]' scene=''>		<StructureSection load='7xo7' size='340' side='right'caption='[[7xo7]], [[Resolution\|resolution]] 3.38Å' 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'>[[7xo7]] 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=7XO7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XO7 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=7xo7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xo7 OCA], [https://pdbe.org/7xo7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xo7 RCSB], [https://www.ebi.ac.uk/pdbsum/7xo7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xo7 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7xo7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xo7 OCA], [https://pdbe.org/7xo7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xo7 RCSB], [https://www.ebi.ac.uk/pdbsum/7xo7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xo7 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]
			== 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: Liu H]]
			[[Category: Wu C]]
			[[Category: Xu HE]]
			[[Category: Xu Y]]
			[[Category: Yin W]]

OCA at 05:12, 15 June 2022

2022-06-15T05:12:48Z

← Older revision		Revision as of 05:12, 15 June 2022
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 7xo7 ~~is ON HOLD~~		====
			<StructureSection load='7xo7' size='340' side='right'caption='[[7xo7]]' scene=''>
	~~Authors~~: ~~Xu, Y~~.~~, Wu, C~~.~~, Liu, H~~.~~, Yin, W~~.~~, Xu, E~~.		== 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~~: ~~SARS-CoV-2 Omicron BA~~.~~2 Variant Spike Trimer with two human ACE2 Bound~~		</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=7xo7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xo7 OCA], [https://pdbe.org/7xo7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xo7 RCSB], [https://www.ebi.ac.uk/pdbsum/7xo7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xo7 ProSAT]</span></td></tr>
	[[~~Category~~: ~~Unreleased Structures~~]]		</table>
	[~~[Category~~: ~~Yin~~, ~~W]]~~		__TOC__
	[~~[Category~~: Xu, ~~E]]~~		</StructureSection>
	[~~[Category~~: ~~Liu, H]~~]		[[Category: Large Structures]]
	[[Category: ~~Wu, C~~]]		[[Category: Z-disk]]
	[[Category: ~~Xu, Y~~]]

OCA: Protected "7xo7" [edit=sysop:move=sysop]

2022-05-12T04:56:18Z

Protected "7xo7" [edit=sysop:move=sysop]

← Older revision	Revision as of 04:56, 12 May 2022
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7xo7 is ON HOLD Authors: Xu, Y., Wu, C., Liu, H., Yin, W., Xu, E. Description: SARS-CoV-2 Omicron BA.2 Variant Spike Trimer with two human ACE2 Bou...

2022-05-12T04:56:17Z

New page: '''Unreleased structure''' The entry 7xo7 is ON HOLD Authors: Xu, Y., Wu, C., Liu, H., Yin, W., Xu, E. Description: SARS-CoV-2 Omicron BA.2 Variant Spike Trimer with two human ACE2 Bou...

New page

'''Unreleased structure'''

The entry 7xo7 is ON HOLD

Authors: Xu, Y., Wu, C., Liu, H., Yin, W., Xu, E.

Description: SARS-CoV-2 Omicron BA.2 Variant Spike Trimer with two human ACE2 Bound
[[Category: Unreleased Structures]]
[[Category: Yin, W]]
[[Category: Xu, E]]
[[Category: Liu, H]]
[[Category: Wu, C]]
[[Category: Xu, Y]]