7beh - Revision history

OCA at 08:36, 17 October 2024

2024-10-17T08:36:18Z

← Older revision		Revision as of 08:36, 17 October 2024
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	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7beh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7beh OCA], [https://pdbe.org/7beh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7beh RCSB], [https://www.ebi.ac.uk/pdbsum/7beh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7beh 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=7beh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7beh OCA], [https://pdbe.org/7beh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7beh RCSB], [https://www.ebi.ac.uk/pdbsum/7beh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7beh 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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 12:26, 1 February 2024

2024-02-01T12:26:51Z

← Older revision		Revision as of 12:26, 1 February 2024
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	====		==Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-316 Fab==
	<StructureSection load='7beh' size='340' side='right'caption='[[7beh]]' scene=''>		<StructureSection load='7beh' size='340' side='right'caption='[[7beh]], [[Resolution\|resolution]] 2.30Å' 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'>[[7beh]] 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=7BEH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BEH 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=7beh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7beh OCA], [https://pdbe.org/7beh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7beh RCSB], [https://www.ebi.ac.uk/pdbsum/7beh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7beh 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]] 2.3Å</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=7beh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7beh OCA], [https://pdbe.org/7beh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7beh RCSB], [https://www.ebi.ac.uk/pdbsum/7beh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7beh 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 ==
			Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here, we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike and focus mainly on 80 that bind the receptor binding domain (RBD). We devise a competition data-driven method to map RBD binding sites. We find that although antibody binding sites are widely dispersed, neutralizing antibody binding is focused, with nearly all highly inhibitory mAbs (IC(50) < 0.1 mug/mL) blocking receptor interaction, except for one that binds a unique epitope in the N-terminal domain. Many of these neutralizing mAbs use public V-genes and are close to germline. We dissect the structural basis of recognition for this large panel of antibodies through X-ray crystallography and cryoelectron microscopy of 19 Fab-antigen structures. We find novel binding modes for some potently inhibitory antibodies and demonstrate that strongly neutralizing mAbs protect, prophylactically or therapeutically, in animal models.

			The antigenic anatomy of SARS-CoV-2 receptor binding domain.,Dejnirattisai W, Zhou D, Ginn HM, Duyvesteyn HME, Supasa P, Case JB, Zhao Y, Walter TS, Mentzer AJ, Liu C, Wang B, Paesen GC, Slon-Campos J, Lopez-Camacho C, Kafai NM, Bailey AL, Chen RE, Ying B, Thompson C, Bolton J, Fyfe A, Gupta S, Tan TK, Gilbert-Jaramillo J, James W, Knight M, Carroll MW, Skelly D, Dold C, Peng Y, Levin R, Dong T, Pollard AJ, Knight JC, Klenerman P, Temperton N, Hall DR, Williams MA, Paterson NG, Bertram FKR, Siebert CA, Clare DK, Howe A, Radecke J, Song Y, Townsend AR, Huang KA, Fry EE, Mongkolsapaya J, Diamond MS, Ren J, Stuart DI, Screaton GR Cell. 2021 Apr 15;184(8):2183-2200.e22. doi: 10.1016/j.cell.2021.02.032. Epub , 2021 Feb 18. PMID:33756110<ref>PMID:33756110</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7beh" 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: Ren J]]
			[[Category: Stuart D]]
			[[Category: Zhao Y]]
			[[Category: Zhou D]]

OCA at 14:44, 3 March 2021

2021-03-03T14:44:49Z

← Older revision		Revision as of 14:44, 3 March 2021
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	~~'''Unreleased structure'''~~

	~~The entry~~ 7beh ~~is ON HOLD until Paper Publication~~		====
			<StructureSection load='7beh' size='340' side='right'caption='[[7beh]]' scene=''>
	~~Authors~~: ~~Zhou, D~~.~~, Zhao, Y~~.~~, Ren, J~~.~~, Stuart, D~~.		== 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 receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-316 Fab~~		</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=7beh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7beh OCA], [https://pdbe.org/7beh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7beh RCSB], [https://www.ebi.ac.uk/pdbsum/7beh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7beh ProSAT]</span></td></tr>
	[~~[Category~~: ~~Unreleased Structures]~~]		</table>
	[[~~Category~~: ~~Ren~~, J]]		__TOC__
	[[~~Category~~: ~~Stuart, D]~~]		</StructureSection>
	[[Category: ~~Zhou, D~~]]		[[Category: Large Structures]]
	[[Category: ~~Zhao, Y~~]]		[[Category: Z-disk]]

OCA at 06:37, 20 January 2021

2021-01-20T06:37:38Z

← Older revision		Revision as of 06:37, 20 January 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7beh is ON HOLD		The entry 7beh is ON HOLD until Paper Publication

	Authors: Zhou, D., Zhao, Y., Ren, J., Stuart, D.		Authors: Zhou, D., Zhao, Y., Ren, J., Stuart, D.

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

2020-12-30T05:19:35Z

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

← Older revision	Revision as of 05:19, 30 December 2020
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7beh is ON HOLD Authors: Zhou, D., Zhao, Y., Ren, J., Stuart, D. Description: Crystal structure of the receptor binding domain of SARS-CoV-2 Spike ...

2020-12-30T05:19:34Z

New page: '''Unreleased structure''' The entry 7beh is ON HOLD Authors: Zhou, D., Zhao, Y., Ren, J., Stuart, D. Description: Crystal structure of the receptor binding domain of SARS-CoV-2 Spike ...

New page

'''Unreleased structure'''

The entry 7beh is ON HOLD

Authors: Zhou, D., Zhao, Y., Ren, J., Stuart, D.

Description: Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-316 Fab
[[Category: Unreleased Structures]]
[[Category: Ren, J]]
[[Category: Stuart, D]]
[[Category: Zhou, D]]
[[Category: Zhao, Y]]