7xu6 - Revision history

OCA at 05:04, 8 September 2022

OCA — Thu, 08 Sep 2022 05:04:04 GMT

←Older revision		Revision as of 05:04, 8 September 2022
Line 3:		Line 3:
	<StructureSection load='7xu6' size='340' side='right'caption='[[7xu6]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='7xu6' size='340' side='right'caption='[[7xu6]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7xu6]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XU6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XU6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7xu6]] is a 3 chain structure with sequence from [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=7XU6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XU6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</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=7xu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xu6 OCA], [https://pdbe.org/7xu6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xu6 RCSB], [https://www.ebi.ac.uk/pdbsum/7xu6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xu6 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=7xu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xu6 OCA], [https://pdbe.org/7xu6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xu6 RCSB], [https://www.ebi.ac.uk/pdbsum/7xu6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xu6 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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Briggs~~, J A.G~~]]	+	[[Category: Severe acute respiratory syndrome coronavirus 2]]
-	[[Category: Carter~~, A P~~]]	+	[[Category: Briggs JAG]]
-	[[Category: Chen, Q]]	+	[[Category: Carter AP]]
-	[[Category: Ciazynska~~, K A~~]]	+	[[Category: Chen Q]]
-	[[Category: Guan, J]]	+	[[Category: Ciazynska KA]]
-	[[Category: He, J]]	+	[[Category: Guan J]]
-	[[Category: He, Y]]	+	[[Category: He J]]
-	[[Category: Liu, B]]	+	[[Category: He Y]]
-	[[Category: Liu, T]]	+	[[Category: Liu B]]
-	[[Category: Qu, K]]	+	[[Category: Liu T]]
-	[[Category: Wang, J]]	+	[[Category: Qu K]]
-	[[Category: Xiong, X]]	+	[[Category: Wang J]]
-	[[Category: Zhang, X]]	+	[[Category: Xiong X]]
-	~~[[Category: Protein engineering]]~~	+	[[Category: Zhang X]]
-	~~[[Category: Sars-cov-2]]~~	+
-	~~[[Category: Spike protein]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 06:47, 18 August 2022

OCA — Thu, 18 Aug 2022 06:47:43 GMT

←Older revision		Revision as of 06:47, 18 August 2022
Line 1:		Line 1:

	==Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), incubated in Low pH after 40-Day Storage in PBS, Locked-2 Conformation==		==Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), incubated in Low pH after 40-Day Storage in PBS, Locked-2 Conformation==
-	<StructureSection load='7xu6' size='340' side='right'caption='[[7xu6]]' scene=''>	+	<StructureSection load='7xu6' size='340' side='right'caption='[[7xu6]], [[Resolution\|resolution]] 2.90Å' 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=7XU6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XU6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7xu6]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XU6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XU6 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=7xu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xu6 OCA], [https://pdbe.org/7xu6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xu6 RCSB], [https://www.ebi.ac.uk/pdbsum/7xu6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xu6 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=BLA:BILIVERDINE+IX+ALPHA'>BLA</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=7xu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xu6 OCA], [https://pdbe.org/7xu6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xu6 RCSB], [https://www.ebi.ac.uk/pdbsum/7xu6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xu6 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 spike (S) protein of SARS-CoV-2 has been observed in three distinct pre-fusion conformations: locked, closed and open. Of these, the function of the locked conformation remains poorly understood. Here we engineered a SARS-CoV-2 S protein construct "S-R/x3" to arrest SARS-CoV-2 spikes in the locked conformation by a disulfide bond. Using this construct we determined high-resolution structures confirming that the x3 disulfide bond has the ability to stabilize the otherwise transient locked conformations. Structural analyses reveal that wild-type SARS-CoV-2 spike can adopt two distinct locked-1 and locked-2 conformations. For the D614G spike, based on which all variants of concern were evolved, only the locked-2 conformation was observed. Analysis of the structures suggests that rigidified domain D in the locked conformations interacts with the hinge to domain C and thereby restrains RBD movement. Structural change in domain D correlates with spike conformational change. We propose that the locked-1 and locked-2 conformations of S are present in the acidic high-lipid cellular compartments during virus assembly and egress. In this model, release of the virion into the neutral pH extracellular space would favour transition to the closed or open conformations. The dynamics of this transition can be altered by mutations that modulate domain D structure, as is the case for the D614G mutation, leading to changes in viral fitness. The S-R/x3 construct provides a tool for the further structural and functional characterization of the locked conformations of S, as well as how sequence changes might alter S assembly and regulation of receptor binding domain dynamics.
		+
		+	Engineered disulfide reveals structural dynamics of locked SARS-CoV-2 spike.,Qu K, Chen Q, Ciazynska KA, Liu B, Zhang X, Wang J, He Y, Guan J, He J, Liu T, Zhang X, Carter AP, Xiong X, Briggs JAG PLoS Pathog. 2022 Jul 29;18(7):e1010583. doi: 10.1371/journal.ppat.1010583., eCollection 2022 Jul. PMID:35905112<ref>PMID:35905112</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7xu6" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Briggs ~~JAG~~]]	+	[[Category: Briggs, J A.G]]
-	[[Category: Carter AP]]	+	[[Category: Carter, A P]]
-	[[Category: Chen Q]]	+	[[Category: Chen, Q]]
-	[[Category: Ciazynska KA]]	+	[[Category: Ciazynska, K A]]
-	[[Category: Guan J]]	+	[[Category: Guan, J]]
-	[[Category: He J]]	+	[[Category: He, J]]
-	[[Category: He Y]]	+	[[Category: He, Y]]
-	[[Category: Liu B]]	+	[[Category: Liu, B]]
-	[[Category: Liu T]]	+	[[Category: Liu, T]]
-	[[Category: Qu K]]	+	[[Category: Qu, K]]
-	[[Category: Wang J]]	+	[[Category: Wang, J]]
-	[[Category: Xiong X]]	+	[[Category: Xiong, X]]
-	[[Category: Zhang X]]	+	[[Category: Zhang, X]]
		+	[[Category: Protein engineering]]
		+	[[Category: Sars-cov-2]]
		+	[[Category: Spike protein]]
		+	[[Category: Viral protein]]

OCA at 06:56, 20 July 2022

OCA — Wed, 20 Jul 2022 06:56:48 GMT

←Older revision		Revision as of 06:56, 20 July 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7xu6 is ON HOLD~~	+	==Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), incubated in Low pH after 40-Day Storage in PBS, Locked-2 Conformation==
-		+	<StructureSection load='7xu6' size='340' side='right'caption='[[7xu6]]' scene=''>
-	~~Authors: Qu, K., Chen, Q., Ciazynska, K.A., Liu, B., Zhang, X., Wang, J., He, Y., Guan, J., He, J., Liu, T., Zhang, X., Carter, A.P., Xiong, X., Briggs, J.A.G.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XU6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XU6 FirstGlance]. <br>
-	~~Description:~~ Structure of SARS-CoV-2 Spike Protein with Engineered ~~disulfide~~ (x3 ~~disulfide-bond mutation-~~D427C, V987C, and single Arg S1/S2 cleavage site), ~~Locked-2 Conformation~~ in Low pH ~~for~~ 40 ~~Days~~ Storage	+	</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=7xu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xu6 OCA], [https://pdbe.org/7xu6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xu6 RCSB], [https://www.ebi.ac.uk/pdbsum/7xu6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xu6 ProSAT]</span></td></tr>
-	[[~~Category: Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Qu, K]~~]	+	__TOC__
-	[[~~Category~~: ~~Briggs~~, J.A.G]]	+	</StructureSection>
-	[[Category: ~~Ciazynska, K.A~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~He, Y~~]]	+	[[Category: Briggs JAG]]
-	[[Category: ~~Liu, B~~]]	+	[[Category: Carter AP]]
-	[[Category: ~~Zhang, X~~]]	+	[[Category: Chen Q]]
-	[[Category: ~~Liu, T~~]]	+	[[Category: Ciazynska KA]]
-	[[Category: Guan, J]]	+	[[Category: Guan J]]
-	[[Category: ~~Carter, A.P~~]]	+	[[Category: He J]]
-	[[Category: He~~, J~~]]	+	[[Category: He Y]]
-	[[Category: ~~Xiong, X~~]]	+	[[Category: Liu B]]
-	[[Category: ~~Chen, Q~~]]	+	[[Category: Liu T]]
-	[[Category: Wang, J]]	+	[[Category: Qu K]]
		+	[[Category: Wang J]]
		+	[[Category: Xiong X]]
		+	[[Category: Zhang X]]

OCA: Protected "7xu6" [edit=sysop:move=sysop]

OCA — Wed, 25 May 2022 06:48:35 GMT

Protected "7xu6" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:48, 25 May 2022

OCA: New page: '''Unreleased structure''' The entry 7xu6 is ON HOLD Authors: Qu, K., Chen, Q., Ciazynska, K.A., Liu, B., Zhang, X., Wang, J., He, Y., Guan, J., He, J., Liu, T., Zhang, X., Carter, A.P....

OCA — Wed, 25 May 2022 06:48:34 GMT

New page: '''Unreleased structure''' The entry 7xu6 is ON HOLD Authors: Qu, K., Chen, Q., Ciazynska, K.A., Liu, B., Zhang, X., Wang, J., He, Y., Guan, J., He, J., Liu, T., Zhang, X., Carter, A.P....

New page

'''Unreleased structure'''

The entry 7xu6 is ON HOLD

Authors: Qu, K., Chen, Q., Ciazynska, K.A., Liu, B., Zhang, X., Wang, J., He, Y., Guan, J., He, J., Liu, T., Zhang, X., Carter, A.P., Xiong, X., Briggs, J.A.G.

Description: Structure of SARS-CoV-2 Spike Protein with Engineered disulfide (x3 disulfide-bond mutation-D427C, V987C, and single Arg S1/S2 cleavage site), Locked-2 Conformation in Low pH for 40 Days Storage
[[Category: Unreleased Structures]]
[[Category: Qu, K]]
[[Category: Briggs, J.A.G]]
[[Category: Ciazynska, K.A]]
[[Category: He, Y]]
[[Category: Liu, B]]
[[Category: Zhang, X]]
[[Category: Liu, T]]
[[Category: Guan, J]]
[[Category: Carter, A.P]]
[[Category: He, J]]
[[Category: Xiong, X]]
[[Category: Chen, Q]]
[[Category: Wang, J]]