6zfo - Revision history

OCA at 15:33, 22 December 2021

2021-12-22T15:33:22Z

←Older revision		Revision as of 15:33, 22 December 2021
Line 1:		Line 1:

-	==~~Association of two complexes of largely structurally disordered Spike ectodomain with bound EY6A Fab~~==	+	====
-	<StructureSection load='6zfo' size='340' side='right'caption='[[6zfo]]~~, [[Resolution\|resolution]] 4.40Å~~' scene=''>	+	<StructureSection load='6zfo' size='340' side='right'caption='[[6zfo]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[6zfo]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/2019-ncov 2019-ncov] and [http://en.wikipedia.org/wiki/Human Human].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=~~6ZFO~~ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=~~6ZFO~~ FirstGlance]. <br>	+	<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>
-	</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>~~	+	</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=6zfo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zfo OCA], [https://pdbe.org/6zfo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zfo RCSB], [https://www.ebi.ac.uk/pdbsum/6zfo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zfo ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6zcz\|6zcz]], [[6zhd\|6zhd]], [[6zdg\|6zdg]], [[6zer\|6zer]]</td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">S, 2 ([http://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'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6zfo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zfo OCA], [~~http~~://pdbe.org/6zfo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6zfo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6zfo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6zfo ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Function ==
-	[[http://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 COVID-19 pandemic has had an unprecedented health and economic impact and there are currently no approved therapies. We have isolated an antibody, EY6A, from an individual convalescing from COVID-19 and have shown that it neutralizes SARS-CoV-2 and cross-reacts with SARS-CoV-1. EY6A Fab binds the receptor binding domain (RBD) of the viral spike glycoprotein tightly (KD of 2 nM), and a 2.6-A-resolution crystal structure of an RBD-EY6A Fab complex identifies the highly conserved epitope, away from the ACE2 receptor binding site. Residues within this footprint are key to stabilizing the pre-fusion spike. Cryo-EM analyses of the pre-fusion spike incubated with EY6A Fab reveal a complex of the intact spike trimer with three Fabs bound and two further multimeric forms comprising the destabilized spike attached to Fab. EY6A binds what is probably a major neutralizing epitope, making it a candidate therapeutic for COVID-19.
-
-	Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient.,Zhou D, Duyvesteyn HME, Chen CP, Huang CG, Chen TH, Shih SR, Lin YC, Cheng CY, Cheng SH, Huang YC, Lin TY, Ma C, Huo J, Carrique L, Malinauskas T, Ruza RR, Shah PNM, Tan TK, Rijal P, Donat RF, Godwin K, Buttigieg KR, Tree JA, Radecke J, Paterson NG, Supasa P, Mongkolsapaya J, Screaton GR, Carroll MW, Gilbert-Jaramillo J, Knight ML, James W, Owens RJ, Naismith JH, Townsend AR, Fry EE, Zhao Y, Ren J, Stuart DI, Huang KA Nat Struct Mol Biol. 2020 Jul 31. pii: 10.1038/s41594-020-0480-y. doi:, 10.1038/s41594-020-0480-y. PMID:32737466<ref>PMID:32737466</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6zfo" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 2019-ncov]]
-	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Duyvesteyn, H M.E]]~~	+	[[Category: Z-disk]]
-	~~[[Category: Fry, E E]]~~	+
-	~~[[Category: Ren, J]]~~	+
-	~~[[Category: Stuart, D I]]~~	+
-	~~[[Category: Zhao, Y]]~~	+
-	~~[[Category: Zhou, D]]~~	+
-	~~[[Category: Ey6a]]~~	+
-	~~[[Category: Human neutralizing antibody]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Rbd]]~~	+
-	~~[[Category: Sars~~-~~cov-2]]~~	+
-	~~[[Category: Spike glycoprotein]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 10:09, 12 August 2020

2020-08-12T10:09:51Z

←Older revision		Revision as of 10:09, 12 August 2020
Line 1:		Line 1:

	==Association of two complexes of largely structurally disordered Spike ectodomain with bound EY6A Fab==		==Association of two complexes of largely structurally disordered Spike ectodomain with bound EY6A Fab==
-	<StructureSection load='6zfo' size='340' side='right'caption='[[6zfo]]' scene=''>	+	<StructureSection load='6zfo' size='340' side='right'caption='[[6zfo]], [[Resolution\|resolution]] 4.40Å' 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=6ZFO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZFO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zfo]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/2019-ncov 2019-ncov] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZFO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZFO 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=6zfo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zfo OCA], [http://pdbe.org/6zfo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zfo RCSB], [http://www.ebi.ac.uk/pdbsum/6zfo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zfo 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">[[6zcz\|6zcz]], [[6zhd\|6zhd]], [[6zdg\|6zdg]], [[6zer\|6zer]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">S, 2 ([http://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'>[http://proteopedia.org/fgij/fg.htm?mol=6zfo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zfo OCA], [http://pdbe.org/6zfo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zfo RCSB], [http://www.ebi.ac.uk/pdbsum/6zfo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zfo ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://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 COVID-19 pandemic has had an unprecedented health and economic impact and there are currently no approved therapies. We have isolated an antibody, EY6A, from an individual convalescing from COVID-19 and have shown that it neutralizes SARS-CoV-2 and cross-reacts with SARS-CoV-1. EY6A Fab binds the receptor binding domain (RBD) of the viral spike glycoprotein tightly (KD of 2 nM), and a 2.6-A-resolution crystal structure of an RBD-EY6A Fab complex identifies the highly conserved epitope, away from the ACE2 receptor binding site. Residues within this footprint are key to stabilizing the pre-fusion spike. Cryo-EM analyses of the pre-fusion spike incubated with EY6A Fab reveal a complex of the intact spike trimer with three Fabs bound and two further multimeric forms comprising the destabilized spike attached to Fab. EY6A binds what is probably a major neutralizing epitope, making it a candidate therapeutic for COVID-19.
		+
		+	Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient.,Zhou D, Duyvesteyn HME, Chen CP, Huang CG, Chen TH, Shih SR, Lin YC, Cheng CY, Cheng SH, Huang YC, Lin TY, Ma C, Huo J, Carrique L, Malinauskas T, Ruza RR, Shah PNM, Tan TK, Rijal P, Donat RF, Godwin K, Buttigieg KR, Tree JA, Radecke J, Paterson NG, Supasa P, Mongkolsapaya J, Screaton GR, Carroll MW, Gilbert-Jaramillo J, Knight ML, James W, Owens RJ, Naismith JH, Townsend AR, Fry EE, Zhao Y, Ren J, Stuart DI, Huang KA Nat Struct Mol Biol. 2020 Jul 31. pii: 10.1038/s41594-020-0480-y. doi:, 10.1038/s41594-020-0480-y. PMID:32737466<ref>PMID:32737466</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6zfo" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: 2019-ncov]]
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Duyvesteyn ~~HME~~]]	+	[[Category: Duyvesteyn, H M.E]]
-	[[Category: Fry EE]]	+	[[Category: Fry, E E]]
-	[[Category: Ren J]]	+	[[Category: Ren, J]]
-	[[Category: Stuart DI]]	+	[[Category: Stuart, D I]]
-	[[Category: Zhao Y]]	+	[[Category: Zhao, Y]]
-	[[Category: Zhou D]]	+	[[Category: Zhou, D]]
		+	[[Category: Ey6a]]
		+	[[Category: Human neutralizing antibody]]
		+	[[Category: Immune system]]
		+	[[Category: Rbd]]
		+	[[Category: Sars-cov-2]]
		+	[[Category: Spike glycoprotein]]
		+	[[Category: Viral protein]]

OCA at 14:12, 8 July 2020

2020-07-08T14:12:43Z

←Older revision		Revision as of 14:12, 8 July 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6zfo ~~is ON HOLD~~	+	==Association of two complexes of largely structurally disordered Spike ectodomain with bound EY6A Fab==
-		+	<StructureSection load='6zfo' size='340' side='right'caption='[[6zfo]]' scene=''>
-	~~Authors~~: ~~Duyvesteyn, H~~.M.E., ~~Zhou, D~~., ~~Zhao, Y~~., ~~Fry, E~~.E., ~~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=6ZFO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZFO FirstGlance]. <br>
-	~~Description: Association of two complexes of largely structurally disordered Spike ectodomain with bound EY6A Fab~~	+	</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=6zfo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zfo OCA], [http://pdbe.org/6zfo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zfo RCSB], [http://www.ebi.ac.uk/pdbsum/6zfo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zfo ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Duyvesteyn~~, H.M.E~~]]	+	__TOC__
-	[[Category: Fry~~, E.E~~]]	+	</StructureSection>
-	[[Category: ~~Zhou, D~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Ren, J~~]]	+	[[Category: Duyvesteyn HME]]
-	[[Category: Zhao, Y]]	+	[[Category: Fry EE]]
-	[[Category: ~~Stuart,~~ D.I]]	+	[[Category: Ren J]]
		+	[[Category: Stuart DI]]
		+	[[Category: Zhao Y]]
		+	[[Category: Zhou D]]

OCA: Protected "6zfo" [edit=sysop:move=sysop]

2020-06-24T18:44:54Z

Protected "6zfo" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:44, 24 June 2020

OCA: New page: '''Unreleased structure''' The entry 6zfo is ON HOLD Authors: Duyvesteyn, H.M.E., Zhou, D., Zhao, Y., Fry, E.E., Ren, J., Stuart, D.I. Description: Association of two complexes of larg...

2020-06-24T18:44:53Z

New page: '''Unreleased structure''' The entry 6zfo is ON HOLD Authors: Duyvesteyn, H.M.E., Zhou, D., Zhao, Y., Fry, E.E., Ren, J., Stuart, D.I. Description: Association of two complexes of larg...

New page

'''Unreleased structure'''

The entry 6zfo is ON HOLD

Authors: Duyvesteyn, H.M.E., Zhou, D., Zhao, Y., Fry, E.E., Ren, J., Stuart, D.I.

Description: Association of two complexes of largely structurally disordered Spike ectodomain with bound EY6A Fab
[[Category: Unreleased Structures]]
[[Category: Duyvesteyn, H.M.E]]
[[Category: Fry, E.E]]
[[Category: Zhou, D]]
[[Category: Ren, J]]
[[Category: Zhao, Y]]
[[Category: Stuart, D.I]]