7k9z - Revision history

OCA at 15:20, 18 October 2023

OCA — Wed, 18 Oct 2023 15:20:14 GMT

←Older revision		Revision as of 15:20, 18 October 2023
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-	====	+	==Crystal structure of SARS-CoV-2 receptor binding domain in complex with the Fab fragments of neutralizing antibodies 298 and 52==
-	<StructureSection load='7k9z' size='340' side='right'caption='[[7k9z]]' scene=''>	+	<StructureSection load='7k9z' size='340' side='right'caption='[[7k9z]], [[Resolution\|resolution]] 2.95Å' 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'>[[7k9z]] 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=7K9Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7K9Z 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=7k9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k9z OCA], [https://pdbe.org/7k9z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7k9z RCSB], [https://www.ebi.ac.uk/pdbsum/7k9z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7k9z ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.95Å</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7k9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k9z OCA], [https://pdbe.org/7k9z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7k9z RCSB], [https://www.ebi.ac.uk/pdbsum/7k9z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7k9z 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, the virus responsible for COVID-19, has caused a global pandemic. Antibodies can be powerful biotherapeutics to fight viral infections. Here, we use the human apoferritin protomer as a modular subunit to drive oligomerization of antibody fragments and transform antibodies targeting SARS-CoV-2 into exceptionally potent neutralizers. Using this platform, half-maximal inhibitory concentration (IC(50)) values as low as 9 x 10(-)(14) M are achieved as a result of up to 10,000-fold potency enhancements compared to corresponding IgGs. Combination of three different antibody specificities and the fragment crystallizable (Fc) domain on a single multivalent molecule conferred the ability to overcome viral sequence variability together with outstanding potency and IgG-like bioavailability. The MULTi-specific, multi-Affinity antiBODY (Multabody or MB) platform thus uniquely leverages binding avidity together with multi-specificity to deliver ultrapotent and broad neutralizers against SARS-CoV-2. The modularity of the platform also makes it relevant for rapid evaluation against other infectious diseases of global health importance. Neutralizing antibodies are a promising therapeutic for SARS-CoV-2.
		+
		+	Multivalency transforms SARS-CoV-2 antibodies into ultrapotent neutralizers.,Rujas E, Kucharska I, Tan YZ, Benlekbir S, Cui H, Zhao T, Wasney GA, Budylowski P, Guvenc F, Newton JC, Sicard T, Semesi A, Muthuraman K, Nouanesengsy A, Aschner CB, Prieto K, Bueler SA, Youssef S, Liao-Chan S, Glanville J, Christie-Holmes N, Mubareka S, Gray-Owen SD, Rubinstein JL, Treanor B, Julien JP Nat Commun. 2021 Jun 16;12(1):3661. doi: 10.1038/s41467-021-23825-2. PMID:34135340<ref>PMID:34135340</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7k9z" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	== 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: Cui H]]
		+	[[Category: Julien JP]]
		+	[[Category: Kucharska I]]
		+	[[Category: Newton JC]]
		+	[[Category: Rujas E]]

OCA at 08:03, 27 January 2021

OCA — Wed, 27 Jan 2021 08:03:29 GMT

←Older revision		Revision as of 08:03, 27 January 2021
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	<StructureSection load='7k9z' size='340' side='right'caption='[[7k9z]]' scene=''>		<StructureSection load='7k9z' size='340' side='right'caption='[[7k9z]]' 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 [~~http~~://proteopedia.org/fgij/fg.htm?mol= 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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=7k9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k9z OCA], [~~http~~://pdbe.org/7k9z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7k9z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7k9z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7k9z ProSAT]</span></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=7k9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k9z OCA], [https://pdbe.org/7k9z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7k9z RCSB], [https://www.ebi.ac.uk/pdbsum/7k9z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7k9z ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 20:38, 28 October 2020

OCA — Wed, 28 Oct 2020 20:38:33 GMT

←Older revision		Revision as of 20:38, 28 October 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 7k9z ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7k9z' size='340' side='right'caption='[[7k9z]]' scene=''>
-	~~Authors~~:	+	== 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 [http://proteopedia.org/fgij/fg.htm?mol= 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=7k9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k9z OCA], [http://pdbe.org/7k9z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7k9z RCSB], [http://www.ebi.ac.uk/pdbsum/7k9z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7k9z ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 04:19, 14 October 2020

OCA — Wed, 14 Oct 2020 04:19:42 GMT

←Older revision		Revision as of 04:19, 14 October 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7k9z is ON HOLD	+	The entry 7k9z is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7k9z" [edit=sysop:move=sysop]

OCA — Wed, 07 Oct 2020 04:50:07 GMT

Protected "7k9z" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:50, 7 October 2020

OCA: New page: '''Unreleased structure''' The entry 7k9z is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 07 Oct 2020 04:50:05 GMT

New page: '''Unreleased structure''' The entry 7k9z is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7k9z is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]