7ul1 - Revision history

OCA at 09:54, 25 October 2023

OCA — Wed, 25 Oct 2023 09:54:51 GMT

←Older revision		Revision as of 09:54, 25 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7ul1]] 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 Severe acute respiratory syndrome coronavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UL1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UL1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7ul1]] 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 Severe acute respiratory syndrome coronavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UL1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UL1 FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.65Å</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=7ul1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ul1 OCA], [https://pdbe.org/7ul1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ul1 RCSB], [https://www.ebi.ac.uk/pdbsum/7ul1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ul1 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=7ul1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ul1 OCA], [https://pdbe.org/7ul1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ul1 RCSB], [https://www.ebi.ac.uk/pdbsum/7ul1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ul1 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:26, 8 March 2023

OCA — Wed, 08 Mar 2023 07:26:59 GMT

←Older revision		Revision as of 07:26, 8 March 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 7ul1 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of SARS-CoV-2 RBD in complex with the neutralizing IGHV3-53-encoded antibody EH3 isolated from a nonvaccinated pediatric patient==
		+	<StructureSection load='7ul1' size='340' side='right'caption='[[7ul1]], [[Resolution\|resolution]] 2.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7ul1]] 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 Severe acute respiratory syndrome coronavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UL1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UL1 FirstGlance]. <br>
		+	</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=7ul1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ul1 OCA], [https://pdbe.org/7ul1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ul1 RCSB], [https://www.ebi.ac.uk/pdbsum/7ul1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ul1 ProSAT]</span></td></tr>
		+	</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 ==
		+	Neutralizing antibodies (NAbs) hold great promise for clinical interventions against SARS-CoV-2 variants of concern (VOCs). Understanding NAb epitope-dependent antiviral mechanisms is crucial for developing vaccines and therapeutics against VOCs. Here we characterized two potent NAbs, EH3 and EH8, isolated from an unvaccinated pediatric patient with exceptional plasma neutralization activity. EH3 and EH8 cross-neutralize the early VOCs and mediate strong Fc-dependent effector activity in vitro. Structural analyses of EH3 and EH8 in complex with the receptor-binding domain (RBD) revealed the molecular determinants of the epitope-driven protection and VOC evasion. While EH3 represents the prevalent IGHV3-53 NAb whose epitope substantially overlaps with the ACE2 binding site, EH8 recognizes a narrow epitope exposed in both RBD-up and RBD-down conformations. When tested in vivo, a single-dose prophylactic administration of EH3 fully protected stringent K18-hACE2 mice from lethal challenge with Delta VOC. Our study demonstrates that protective NAbs responses converge in pediatric and adult SARS-CoV-2 patients.

-	~~Authors: Chen~~, Y., Tolbert, W.D., ~~Pazgier~~, M.	+	Molecular basis for antiviral activity of two pediatric neutralizing antibodies targeting SARS-CoV-2 Spike RBD.,Chen Y, Prevost J, Ullah I, Romero H, Lisi V, Tolbert WD, Grover JR, Ding S, Gong SY, Beaudoin-Bussieres G, Gasser R, Benlarbi M, Vezina D, Anand SP, Chatterjee D, Goyette G, Grunst MW, Yang Z, Bo Y, Zhou F, Beland K, Bai X, Zeher AR, Huang RK, Nguyen DN, Sherburn R, Wu D, Piszczek G, Pare B, Matthies D, Xia D, Richard J, Kumar P, Mothes W, Cote M, Uchil PD, Lavallee VP, Smith MA, Pazgier M, Haddad E, Finzi A iScience. 2023 Jan 20;26(1):105783. doi: 10.1016/j.isci.2022.105783. Epub 2022 , Dec 9. PMID:36514310<ref>PMID:36514310</ref>

-	~~Description: Crystal structure~~ of ~~SARS-CoV-2 RBD in complex with~~ the ~~neutralizing IGHV3~~-53-~~encoded antibody EH3 isolated from a nonvaccinated pediatric patient~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Pazgier, M~~]]	+	<div class="pdbe-citations 7ul1" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Tolbert, W.D~~]]	+	== References ==
-	[[Category: Chen, Y]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
		+	[[Category: Severe acute respiratory syndrome coronavirus]]
		+	[[Category: Chen Y]]
		+	[[Category: Pazgier M]]
		+	[[Category: Tolbert WD]]

OCA at 04:44, 12 May 2022

OCA — Thu, 12 May 2022 04:44:56 GMT

←Older revision		Revision as of 04:44, 12 May 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7ul1 is ON HOLD	+	The entry 7ul1 is ON HOLD until Paper Publication

	Authors: Chen, Y., Tolbert, W.D., Pazgier, M.		Authors: Chen, Y., Tolbert, W.D., Pazgier, M.

OCA: Protected "7ul1" [edit=sysop:move=sysop]

OCA — Wed, 13 Apr 2022 08:34:56 GMT

Protected "7ul1" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:34, 13 April 2022

OCA: New page: '''Unreleased structure''' The entry 7ul1 is ON HOLD Authors: Chen, Y., Tolbert, W.D., Pazgier, M. Description: Crystal structure of SARS-CoV-2 RBD in complex with the neutralizing IGH...

OCA — Wed, 13 Apr 2022 08:34:54 GMT

New page: '''Unreleased structure''' The entry 7ul1 is ON HOLD Authors: Chen, Y., Tolbert, W.D., Pazgier, M. Description: Crystal structure of SARS-CoV-2 RBD in complex with the neutralizing IGH...

New page

'''Unreleased structure'''

The entry 7ul1 is ON HOLD

Authors: Chen, Y., Tolbert, W.D., Pazgier, M.

Description: Crystal structure of SARS-CoV-2 RBD in complex with the neutralizing IGHV3-53-encoded antibody EH3 isolated from a nonvaccinated pediatric patient
[[Category: Unreleased Structures]]
[[Category: Pazgier, M]]
[[Category: Tolbert, W.D]]
[[Category: Chen, Y]]