OCA at 16:10, 18 October 2023

OCA — Wed, 18 Oct 2023 16:10:12 GMT

←Older revision		Revision as of 16:10, 18 October 2023
Line 1:		Line 1:

-	====	+	==Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 47D1==
-	<StructureSection load='7mf1' size='340' side='right'caption='[[7mf1]]' scene=''>	+	<StructureSection load='7mf1' size='340' side='right'caption='[[7mf1]], [[Resolution\|resolution]] 2.09Å' 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'>[[7mf1]] 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=7MF1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MF1 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=7mf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mf1 OCA], [https://pdbe.org/7mf1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mf1 RCSB], [https://www.ebi.ac.uk/pdbsum/7mf1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mf1 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]] 2.092Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <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=7mf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mf1 OCA], [https://pdbe.org/7mf1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mf1 RCSB], [https://www.ebi.ac.uk/pdbsum/7mf1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mf1 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 ==
		+	It is unclear whether individuals with enormous diversity in B cell receptor repertoires are consistently able to mount effective antibody responses against SARS-CoV-2. We analyzed antibody responses in a cohort of 55 convalescent patients and isolated 54 potent neutralizing monoclonal antibodies (mAbs). While most of the mAbs target the angiotensin-converting enzyme 2 (ACE2) binding surface on the receptor binding domain (RBD) of SARS-CoV-2 spike protein, mAb 47D1 binds only to one side of the receptor binding surface on the RBD. Neutralization by 47D1 is achieved independent of interfering RBD-ACE2 binding. A crystal structure of the mAb-RBD complex shows that the IF motif at the tip of 47D1 CDR H2 interacts with a hydrophobic pocket in the RBD. Diverse immunoglobulin gene usage and convergent epitope targeting characterize neutralizing antibody responses to SARS-CoV-2, suggesting that vaccines that effectively present the receptor binding site on the RBD will likely elicit neutralizing antibody responses in a large fraction of the population.
		+
		+	Diverse immunoglobulin gene usage and convergent epitope targeting in neutralizing antibody responses to SARS-CoV-2.,Zhou X, Ma F, Xie J, Yuan M, Li Y, Shaabani N, Zhao F, Huang D, Wu NC, Lee CD, Liu H, Li J, Chen Z, Hong Y, Liu WH, Xiao N, Burton DR, Tu H, Li H, Chen X, Teijaro JR, Wilson IA, Xiao C, Huang Z Cell Rep. 2021 May 11;35(6):109109. doi: 10.1016/j.celrep.2021.109109. Epub 2021 , Apr 24. PMID:33932326<ref>PMID:33932326</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7mf1" 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: Wilson IA]]
		+	[[Category: Yuan M]]
		+	[[Category: Zhu X]]

OCA at 09:22, 12 May 2021

OCA — Wed, 12 May 2021 09:22:14 GMT

←Older revision		Revision as of 09:22, 12 May 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7mf1 ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7mf1' size='340' side='right'caption='[[7mf1]]' 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 [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=7mf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mf1 OCA], [https://pdbe.org/7mf1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mf1 RCSB], [https://www.ebi.ac.uk/pdbsum/7mf1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mf1 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA: Protected "7mf1" [edit=sysop:move=sysop]

OCA — Wed, 14 Apr 2021 05:44:54 GMT

Protected "7mf1" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:44, 14 April 2021

OCA: New page: '''Unreleased structure''' The entry 7mf1 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 14 Apr 2021 05:44:53 GMT

New page: '''Unreleased structure''' The entry 7mf1 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7mf1 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]

7mf1 - Revision history

OCA at 16:10, 18 October 2023

OCA at 09:22, 12 May 2021

OCA: Protected "7mf1" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7mf1 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures