7chf - Revision history

OCA at 16:08, 29 November 2023

OCA — Wed, 29 Nov 2023 16:08:12 GMT

←Older revision		Revision as of 16:08, 29 November 2023
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-	====	+	==Crystal structure of the SARS-CoV-2 RBD in complex with BD-604 Fab and BD-368-2 Fab==
-	<StructureSection load='7chf' size='340' side='right'caption='[[7chf]]' scene=''>	+	<StructureSection load='7chf' size='340' side='right'caption='[[7chf]], [[Resolution\|resolution]] 2.67Å' 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'>[[7chf]] 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=7CHF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CHF 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=7chf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7chf OCA], [https://pdbe.org/7chf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7chf RCSB], [https://www.ebi.ac.uk/pdbsum/7chf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7chf 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]] 2.674Å</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=7chf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7chf OCA], [https://pdbe.org/7chf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7chf RCSB], [https://www.ebi.ac.uk/pdbsum/7chf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7chf 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 ==
		+	Understanding how potent neutralizing antibodies (NAbs) inhibit SARS-CoV-2 is critical for effective therapeutic development. We previously described BD-368-2, a SARS-CoV-2 NAb with high potency; however, its neutralization mechanism is largely unknown. Here, we report the 3.5-A cryo-EM structure of BD-368-2/trimeric-spike complex, revealing that BD-368-2 fully blocks ACE2 recognition by occupying all three receptor-binding domains (RBDs) simultaneously, regardless of their "up" or "down" conformations. Also, BD-368-2 treats infected adult hamsters at low dosages and at various administering windows, in contrast to placebo hamsters that manifested severe interstitial pneumonia. Moreover, BD-368-2's epitope completely avoids the common binding site of VH3-53/VH3-66 recurrent NAbs, evidenced by tripartite co-crystal structures with RBDs. Pairing BD-368-2 with a potent recurrent NAb neutralizes SARS-CoV-2 pseudovirus at pM level and rescues mutation-induced neutralization escapes. Together, our results rationalized a new RBD epitope that leads to high neutralization potency and demonstrated BD-368-2's therapeutic potential in treating COVID-19.
		+
		+	Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy.,Du S, Cao Y, Zhu Q, Yu P, Qi F, Wang G, Du X, Bao L, Deng W, Zhu H, Liu J, Nie J, Zheng Y, Liang H, Liu R, Gong S, Xu H, Yisimayi A, Lv Q, Wang B, He R, Han Y, Zhao W, Bai Y, Qu Y, Gao X, Ji C, Wang Q, Gao N, Huang W, Wang Y, Xie XS, Su XD, Xiao J, Qin C Cell. 2020 Sep 14. pii: S0092-8674(20)31232-0. doi: 10.1016/j.cell.2020.09.035. PMID:32970990<ref>PMID:32970990</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7chf" 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: Xiao J]]
		+	[[Category: Zhu Q]]

OCA at 18:02, 10 March 2021

OCA — Wed, 10 Mar 2021 18:02:40 GMT

←Older revision		Revision as of 18:02, 10 March 2021
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	<StructureSection load='7chf' size='340' side='right'caption='[[7chf]]' scene=''>		<StructureSection load='7chf' size='340' side='right'caption='[[7chf]]' 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=7chf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7chf OCA], [~~http~~://pdbe.org/7chf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7chf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7chf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7chf 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=7chf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7chf OCA], [https://pdbe.org/7chf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7chf RCSB], [https://www.ebi.ac.uk/pdbsum/7chf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7chf ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 09:55, 16 September 2020

OCA — Wed, 16 Sep 2020 09:55:50 GMT

←Older revision		Revision as of 09:55, 16 September 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 7chf ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7chf' size='340' side='right'caption='[[7chf]]' scene=''>
-	~~Authors~~: ~~Xiao, J~~.~~, Zhu, Q~~.	+	== 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~~: ~~Crystal structure of the SARS-CoV~~-~~2 RBD in complex with BD-604 Fab and BD-368-2 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=7chf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7chf OCA], [http://pdbe.org/7chf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7chf RCSB], [http://www.ebi.ac.uk/pdbsum/7chf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7chf ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: ~~Xiao, J~~]]	+	__TOC__
-	[[Category: ~~Zhu, Q~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 07:27, 9 September 2020

OCA — Wed, 09 Sep 2020 07:27:31 GMT

←Older revision		Revision as of 07:27, 9 September 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Xiao, J., Zhu, Q.		Authors: Xiao, J., Zhu, Q.

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

OCA — Wed, 22 Jul 2020 08:28:06 GMT

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

←Older revision

Revision as of 08:28, 22 July 2020

OCA: New page: '''Unreleased structure''' The entry 7chf is ON HOLD Authors: Xiao, J., Zhu, Q. Description: Crystal structure of the SARS-CoV-2 RBD in complex with BD-604 Fab and BD-368-2 Fab [[Categ...

OCA — Wed, 22 Jul 2020 08:28:04 GMT

New page: '''Unreleased structure''' The entry 7chf is ON HOLD Authors: Xiao, J., Zhu, Q. Description: Crystal structure of the SARS-CoV-2 RBD in complex with BD-604 Fab and BD-368-2 Fab [[Categ...

New page

'''Unreleased structure'''

The entry 7chf is ON HOLD

Authors: Xiao, J., Zhu, Q.

Description: Crystal structure of the SARS-CoV-2 RBD in complex with BD-604 Fab and BD-368-2 Fab
[[Category: Unreleased Structures]]
[[Category: Xiao, J]]
[[Category: Zhu, Q]]