OCA at 12:31, 1 February 2024

OCA — Thu, 01 Feb 2024 12:31:29 GMT

←Older revision		Revision as of 12:31, 1 February 2024
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-	====	+	==Crystal Structure of the SARS-CoV-2 Receptor Binding Domain in Complex with Antibody ION-300==
-	<StructureSection load='7bnv' size='340' side='right'caption='[[7bnv]]' scene=''>	+	<StructureSection load='7bnv' size='340' side='right'caption='[[7bnv]], [[Resolution\|resolution]] 2.35Å' 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'>[[7bnv]] is a 3 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=7BNV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BNV 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=7bnv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bnv OCA], [https://pdbe.org/7bnv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bnv RCSB], [https://www.ebi.ac.uk/pdbsum/7bnv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bnv 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]] 2.35Å</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=7bnv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bnv OCA], [https://pdbe.org/7bnv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bnv RCSB], [https://www.ebi.ac.uk/pdbsum/7bnv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bnv 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 ==
		+	Passive immunization using monoclonal antibodies will play a vital role in the fight against COVID-19. The recent emergence of viral variants with reduced sensitivity to some current antibodies and vaccines highlights the importance of broad cross-reactivity. This study describes deep-mining of the antibody repertoires of hospitalized COVID-19 patients using phage display technology and B cell receptor (BCR) repertoire sequencing to isolate neutralizing antibodies and gain insights into the early antibody response. This comprehensive discovery approach has yielded a panel of potent neutralizing antibodies which bind distinct viral epitopes including epitopes conserved in SARS-CoV-1. Structural determination of a non-ACE2 receptor blocking antibody reveals a previously undescribed binding epitope, which is unlikely to be affected by the mutations in any of the recently reported major viral variants including B.1.1.7 (from the UK), B.1.351 (from South Africa) and B.1.1.28 (from Brazil). Finally, by combining sequences of the RBD binding and neutralizing antibodies with the B cell receptor repertoire sequencing, we also describe a highly convergent early antibody response. Similar IgM-derived sequences occur within this study group and also within patient responses described by multiple independent studies published previously.
		+
		+	Cross-Reactive SARS-CoV-2 Neutralizing Antibodies From Deep Mining of Early Patient Responses.,Bullen G, Galson JD, Hall G, Villar P, Moreels L, Ledsgaard L, Mattiuzzo G, Bentley EM, Masters EW, Tang D, Millett S, Tongue D, Brown R, Diamantopoulos I, Parthiban K, Tebbutt C, Leah R, Chaitanya K, Ergueta-Carballo S, Pazeraitis D, Surade SB, Ashiru O, Crippa L, Cowan R, Bowler MW, Campbell JI, Lee WJ, Carr MD, Matthews D, Pfeffer P, Hufton SE, Sawmynaden K, Osbourn J, McCafferty J, Karatt-Vellatt A Front Immunol. 2021 Jun 15;12:678570. doi: 10.3389/fimmu.2021.678570. eCollection , 2021. PMID:34211469<ref>PMID:34211469</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7bnv" 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: Carr M]]
		+	[[Category: Cowan R]]
		+	[[Category: Hall G]]

OCA at 13:34, 17 November 2021

OCA — Wed, 17 Nov 2021 13:34:49 GMT

←Older revision		Revision as of 13:34, 17 November 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7bnv ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7bnv' size='340' side='right'caption='[[7bnv]]' scene=''>
-	~~Authors~~: ~~Hall, G~~.~~, Cowan, R~~.~~, Carr, M~~.	+	== 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>
-	~~Description: Crystal Structure of the SARS~~-~~CoV-2 Receptor Binding Domain in Complex with Antibody ION-300~~	+	</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=7bnv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bnv OCA], [https://pdbe.org/7bnv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bnv RCSB], [https://www.ebi.ac.uk/pdbsum/7bnv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bnv ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Cowan~~, R]]	+	__TOC__
-	[[Category: ~~Hall, G~~]]	+	</StructureSection>
-	[[Category: ~~Carr, M~~]]	+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 09:05, 10 February 2021

OCA — Wed, 10 Feb 2021 09:05:24 GMT

←Older revision		Revision as of 09:05, 10 February 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Hall, G., Cowan, R., Carr, M.		Authors: Hall, G., Cowan, R., Carr, M.

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

OCA — Wed, 03 Feb 2021 09:14:33 GMT

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

←Older revision

Revision as of 09:14, 3 February 2021

OCA: New page: '''Unreleased structure''' The entry 7bnv is ON HOLD Authors: Hall, G., Cowan, R., Carr, M. Description: Crystal Structure of the SARS-CoV-2 Receptor Binding Domain in Complex with Ant...

OCA — Wed, 03 Feb 2021 09:14:31 GMT

New page: '''Unreleased structure''' The entry 7bnv is ON HOLD Authors: Hall, G., Cowan, R., Carr, M. Description: Crystal Structure of the SARS-CoV-2 Receptor Binding Domain in Complex with Ant...

New page

'''Unreleased structure'''

The entry 7bnv is ON HOLD

Authors: Hall, G., Cowan, R., Carr, M.

Description: Crystal Structure of the SARS-CoV-2 Receptor Binding Domain in Complex with Antibody ION-300
[[Category: Unreleased Structures]]
[[Category: Cowan, R]]
[[Category: Hall, G]]
[[Category: Carr, M]]

7bnv - Revision history

OCA at 12:31, 1 February 2024

OCA at 13:34, 17 November 2021

OCA at 09:05, 10 February 2021

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

OCA: New page: '''Unreleased structure''' The entry 7bnv is ON HOLD Authors: Hall, G., Cowan, R., Carr, M. Description: Crystal Structure of the SARS-CoV-2 Receptor Binding Domain in Complex with Ant...