7jwy - Revision history

OCA at 16:56, 15 December 2021

OCA — Wed, 15 Dec 2021 16:56:59 GMT

←Older revision		Revision as of 16:56, 15 December 2021
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	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	SARS-CoV-2 has emerged as a global pathogen, sparking urgent vaccine development efforts with the trimeric spike. However, the inability of antibodies like CR3022, which binds a cryptic spike epitope with nanomolar affinity, to neutralize virus, suggests a spike-~~based means of neutralization escape. Here, we show the SARS-CoV-2 spike~~ to ~~have 10%~~ the ~~unfolding enthalpy of a globular protein at physiological pH, where it is recognized by antibodies like CR3022,~~ and up to ~~10-times more unfolding enthalpy at endosomal pH~~, ~~where it sheds such antibodies, suggesting that the spike evades potentially neutralizing antibody~~ through a pH-~~dependent mechanism of conformational masking~~. To understand ~~the compatibility of this mechanism with~~ ACE2~~-receptor interactions~~, we ~~carried out binding measurements and~~ determined cryo-EM structures ~~of the~~ spike ~~recognizing~~ up to three ACE2 molecules ~~at both physiological and endosomal pH~~. In the absence of ACE2, ~~cryo~~-~~EM analyses indicated lower pH to reduce conformational heterogeneity. Single-receptor binding domain (~~RBD)-up conformations dominated at pH 5.5, resolving into a ~~locked~~ all-down conformation at lower pH ~~through lowering of RBD and refolding of~~ a pH-dependent ~~switch. Notably,~~ the ~~emerging Asp614Gly strain partially destabilizes~~ the ~~switch~~ that ~~locks RBD~~ down~~, thereby enhancing functional interactions with ACE2 while reducing~~ evasion ~~by conformational masking~~.	+	The SARS-CoV-2 spike employs mobile receptor-binding domains (RBDs) to engage the human ACE2 receptor and to facilitate virus entry, which can occur through low-pH-endosomal pathways. To understand how ACE2 binding and low pH affect spike conformation, we determined cryo-electron microscopy structures-at serological and endosomal pH-delineating spike recognition of up to three ACE2 molecules. RBDs freely adopted "up" conformations required for ACE2 interaction, primarily through RBD movement combined with smaller alterations in neighboring domains. In the absence of ACE2, single-RBD-up conformations dominated at pH 5.5, resolving into a solitary all-down conformation at lower pH. Notably, a pH-dependent refolding region (residues 824-858) at the spike-interdomain interface displayed dramatic structural rearrangements and mediated RBD positioning through coordinated movements of the entire trimer apex. These structures provide a foundation for understanding prefusion-spike mechanics governing endosomal entry; we suggest that the low pH all-down conformation potentially facilitates immune evasion from RBD-up binding antibody.

-	~~A pH~~-~~dependent switch mediates conformational masking~~ of SARS-CoV-2 ~~spike~~.,Zhou T, Tsybovsky Y~~, Olia AS~~, Gorman J, Rapp MA, Cerutti G, Katsamba PS, ~~Nazzari A~~, Schon A~~, Wang PD~~, Bimela J~~, Shi W, Teng IT, Zhang B~~, Boyington JC, ~~Chuang GY~~, ~~Sampson JM~~, Sastry M, Stephens T, Stuckey J, Wang S, Friesner RA, Ho DD, Mascola JR, Shapiro L, Kwong PD ~~bioRxiv~~. 2020 ~~Jul 4~~. doi: 10.~~1101~~/2020.07.04.~~187989~~. PMID:~~32637958~~<ref>PMID:~~32637958~~</ref>	+	Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.,Zhou T, Tsybovsky Y, Gorman J, Rapp M, Cerutti G, Chuang GY, Katsamba PS, Sampson JM, Schon A, Bimela J, Boyington JC, Nazzari A, Olia AS, Shi W, Sastry M, Stephens T, Stuckey J, Teng IT, Wang P, Wang S, Zhang B, Friesner RA, Ho DD, Mascola JR, Shapiro L, Kwong PD Cell Host Microbe. 2020 Dec 9;28(6):867-879.e5. doi: 10.1016/j.chom.2020.11.004. , Epub 2020 Nov 17. PMID:33271067<ref>PMID:33271067</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

OCA at 05:53, 6 October 2021

OCA — Wed, 06 Oct 2021 05:53:34 GMT

←Older revision		Revision as of 05:53, 6 October 2021
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	==Structure of SARS-CoV-2 spike at pH 4.5==		==Structure of SARS-CoV-2 spike at pH 4.5==
-	<StructureSection load='7jwy' size='340' side='right'caption='[[7jwy]]' scene=''>	+	<StructureSection load='7jwy' size='340' side='right'caption='[[7jwy]], [[Resolution\|resolution]] 2.50Å' 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=7JWY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7JWY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7jwy]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/2019-ncov 2019-ncov]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JWY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JWY FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=7jwy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jwy OCA], [~~http~~://pdbe.org/7jwy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7jwy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7jwy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7jwy 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></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6xlu\|6xlu]], [[6xm0\|6xm0]], [[6xm3\|6xm3]], [[6xm4\|6xm4]], [[6xm5\|6xm5]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">S, 2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2697049 2019-nCoV])</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=7jwy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jwy OCA], [https://pdbe.org/7jwy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jwy RCSB], [https://www.ebi.ac.uk/pdbsum/7jwy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jwy 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 ==
		+	SARS-CoV-2 has emerged as a global pathogen, sparking urgent vaccine development efforts with the trimeric spike. However, the inability of antibodies like CR3022, which binds a cryptic spike epitope with nanomolar affinity, to neutralize virus, suggests a spike-based means of neutralization escape. Here, we show the SARS-CoV-2 spike to have 10% the unfolding enthalpy of a globular protein at physiological pH, where it is recognized by antibodies like CR3022, and up to 10-times more unfolding enthalpy at endosomal pH, where it sheds such antibodies, suggesting that the spike evades potentially neutralizing antibody through a pH-dependent mechanism of conformational masking. To understand the compatibility of this mechanism with ACE2-receptor interactions, we carried out binding measurements and determined cryo-EM structures of the spike recognizing up to three ACE2 molecules at both physiological and endosomal pH. In the absence of ACE2, cryo-EM analyses indicated lower pH to reduce conformational heterogeneity. Single-receptor binding domain (RBD)-up conformations dominated at pH 5.5, resolving into a locked all-down conformation at lower pH through lowering of RBD and refolding of a pH-dependent switch. Notably, the emerging Asp614Gly strain partially destabilizes the switch that locks RBD down, thereby enhancing functional interactions with ACE2 while reducing evasion by conformational masking.
		+
		+	A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike.,Zhou T, Tsybovsky Y, Olia AS, Gorman J, Rapp MA, Cerutti G, Katsamba PS, Nazzari A, Schon A, Wang PD, Bimela J, Shi W, Teng IT, Zhang B, Boyington JC, Chuang GY, Sampson JM, Sastry M, Stephens T, Stuckey J, Wang S, Friesner RA, Ho DD, Mascola JR, Shapiro L, Kwong PD bioRxiv. 2020 Jul 4. doi: 10.1101/2020.07.04.187989. PMID:32637958<ref>PMID:32637958</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7jwy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: 2019-ncov]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kwong PD]]	+	[[Category: Kwong, P D]]
-	[[Category: Tsybovsky Y]]	+	[[Category: Tsybovsky, Y]]
-	[[Category: Zhou T]]	+	[[Category: Zhou, T]]
		+	[[Category: Sars-cov-2 covid19]]
		+	[[Category: Viral protein]]

OCA at 06:59, 25 November 2020

OCA — Wed, 25 Nov 2020 06:59:48 GMT

←Older revision		Revision as of 06:59, 25 November 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 7jwy ~~is ON HOLD until Paper Publication~~	+	==Structure of SARS-CoV-2 spike at pH 4.5==
-		+	<StructureSection load='7jwy' size='340' side='right'caption='[[7jwy]]' scene=''>
-	~~Authors~~: ~~Zhou~~, T., ~~Tsybovsky~~, Y., ~~Kwong, P~~.D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JWY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7JWY FirstGlance]. <br>
-	~~Description~~: ~~Structure of SARS~~-~~CoV-2 spike at pH 4~~.5	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7jwy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jwy OCA], [http://pdbe.org/7jwy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7jwy RCSB], [http://www.ebi.ac.uk/pdbsum/7jwy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7jwy ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Kwong~~, P.D~~]]	+	__TOC__
-	[[Category: ~~Zhou, T~~]]	+	</StructureSection>
-	[[Category: ~~Tsybovsky, Y~~]]	+	[[Category: Large Structures]]
		+	[[Category: Kwong PD]]
		+	[[Category: Tsybovsky Y]]
		+	[[Category: Zhou T]]

OCA at 07:02, 16 September 2020

OCA — Wed, 16 Sep 2020 07:02:11 GMT

←Older revision		Revision as of 07:02, 16 September 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Zhou, T., Tsybovsky, Y., Kwong, P.D.		Authors: Zhou, T., Tsybovsky, Y., Kwong, P.D.

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

OCA — Wed, 02 Sep 2020 05:26:03 GMT

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

←Older revision

Revision as of 05:26, 2 September 2020

OCA: New page: '''Unreleased structure''' The entry 7jwy is ON HOLD Authors: Zhou, T., Tsybovsky, Y., Kwong, P.D. Description: Structure of SARS-CoV-2 spike at pH 4.5 [[Category: Unreleased Structure...

OCA — Wed, 02 Sep 2020 05:26:02 GMT

New page: '''Unreleased structure''' The entry 7jwy is ON HOLD Authors: Zhou, T., Tsybovsky, Y., Kwong, P.D. Description: Structure of SARS-CoV-2 spike at pH 4.5 [[Category: Unreleased Structure...

New page

'''Unreleased structure'''

The entry 7jwy is ON HOLD

Authors: Zhou, T., Tsybovsky, Y., Kwong, P.D.

Description: Structure of SARS-CoV-2 spike at pH 4.5
[[Category: Unreleased Structures]]
[[Category: Kwong, P.D]]
[[Category: Zhou, T]]
[[Category: Tsybovsky, Y]]