7byr - Revision history

OCA at 17:58, 10 March 2021

OCA — Wed, 10 Mar 2021 17:58:44 GMT

←Older revision		Revision as of 17:58, 10 March 2021
Line 3:		Line 3:
	<StructureSection load='7byr' size='340' side='right'caption='[[7byr]], [[Resolution\|resolution]] 3.84Å' scene=''>		<StructureSection load='7byr' size='340' side='right'caption='[[7byr]], [[Resolution\|resolution]] 3.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7byr]] is a 5 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=7BYR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7BYR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7byr]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/2019-ncov 2019-ncov] and [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BYR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BYR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</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=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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='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'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=7byr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7byr OCA], [~~http~~://pdbe.org/7byr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7byr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7byr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7byr 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=7byr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7byr OCA], [https://pdbe.org/7byr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7byr RCSB], [https://www.ebi.ac.uk/pdbsum/7byr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7byr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== 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]	+	[[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 ==

OCA at 11:50, 22 July 2020

OCA — Wed, 22 Jul 2020 11:50:28 GMT

←Older revision		Revision as of 11:50, 22 July 2020
Line 1:		Line 1:

	==BD23-Fab in complex with the S ectodomain trimer==		==BD23-Fab in complex with the S ectodomain trimer==
-	<StructureSection load='7byr' size='340' side='right'caption='[[7byr]]' scene=''>	+	<StructureSection load='7byr' size='340' side='right'caption='[[7byr]], [[Resolution\|resolution]] 3.84Å' 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=7BYR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7BYR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7byr]] is a 5 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=7BYR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7BYR 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=7byr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7byr OCA], [http://pdbe.org/7byr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7byr RCSB], [http://www.ebi.ac.uk/pdbsum/7byr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7byr 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=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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=7byr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7byr OCA], [http://pdbe.org/7byr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7byr RCSB], [http://www.ebi.ac.uk/pdbsum/7byr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7byr 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 urgently needs therapeutic and prophylactic interventions. Here we report the rapid identification of SARS-CoV-2 neutralizing antibodies by high-throughput single-cell RNA and VDJ sequencing of antigen-enriched B cells from 60 convalescent patients. From 8,558 antigen-binding IgG1(+) clonotypes, 14 potent neutralizing antibodies were identified with the most potent one, BD-368-2, exhibiting an IC50 of 1.2 ng/mL and 15 ng/mL against pseudotyped and authentic SARS-CoV-2, respectively. BD-368-2 also displayed strong therapeutic and prophylactic efficacy in SARS-CoV-2-infected hACE2-transgenic mice. Additionally, the 3.8A Cryo-EM structure of a neutralizing antibody in complex with the spike-ectodomain trimer revealed the antibody's epitope overlaps with the ACE2 binding site. Moreover, we demonstrated that SARS-CoV-2 neutralizing antibodies could be directly selected based on similarities of their predicted CDR3H structures to those of SARS-CoV neutralizing antibodies. Altogether, we showed that human neutralizing antibodies could be efficiently discovered by high-throughput single B-cell sequencing in response to pandemic infectious diseases.
		+
		+	Potent neutralizing antibodies against SARS-CoV-2 identified by high-throughput single-cell sequencing of convalescent patients' B cells.,Cao Y, Su B, Guo X, Sun W, Deng Y, Bao L, Zhu Q, Zhang X, Zheng Y, Geng C, Chai X, He R, Li X, Lv Q, Zhu H, Deng W, Xu Y, Wang Y, Qiao L, Tan Y, Song L, Wang G, Du X, Gao N, Liu J, Xiao J, Su XD, Du Z, Feng Y, Qin C, Qin C, Jin R, Xie XS Cell. 2020 May 18. pii: S0092-8674(20)30620-6. doi: 10.1016/j.cell.2020.05.025. PMID:32425270<ref>PMID:32425270</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7byr" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: 2019-ncov]]
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Wang G]]	+	[[Category: Wang, G]]
-	[[Category: Xiao J]]	+	[[Category: Xiao, J]]
-	[[Category: Zhu Q]]	+	[[Category: Zhu, Q]]
		+	[[Category: Antigen]]
		+	[[Category: Neutralizing antibody]]
		+	[[Category: Rbd]]
		+	[[Category: Sars-cov-2]]
		+	[[Category: Viral protein]]

OCA at 06:30, 10 June 2020

OCA — Wed, 10 Jun 2020 06:30:36 GMT

←Older revision		Revision as of 06:30, 10 June 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7byr is ~~ON HOLD until Paper Publication~~	+	==BD23-Fab in complex with the S ectodomain trimer==
-		+	<StructureSection load='7byr' size='340' side='right'caption='[[7byr]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BYR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7BYR FirstGlance]. <br>
-	~~Description~~:	+	</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=7byr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7byr OCA], [http://pdbe.org/7byr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7byr RCSB], [http://www.ebi.ac.uk/pdbsum/7byr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7byr ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Wang G]]
		+	[[Category: Xiao J]]
		+	[[Category: Zhu Q]]

OCA at 04:22, 13 May 2020

OCA — Wed, 13 May 2020 04:22:07 GMT

←Older revision		Revision as of 04:22, 13 May 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 29 Apr 2020 05:39:30 GMT

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

←Older revision

Revision as of 05:39, 29 April 2020

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

OCA — Wed, 29 Apr 2020 05:39:28 GMT

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

New page

'''Unreleased structure'''

The entry 7byr is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]