OCA at 15:37, 18 October 2023

2023-10-18T15:37:55Z

←Older revision		Revision as of 15:37, 18 October 2023
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-	====	+	==Structure of SARS-CoV-2 spike RBD in complex with cyclic peptide==
-	<StructureSection load='7l4z' size='340' side='right'caption='[[7l4z]]' scene=''>	+	<StructureSection load='7l4z' size='340' side='right'caption='[[7l4z]], [[Resolution\|resolution]] 3.96Å' 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'>[[7l4z]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2 Severe acute respiratory syndrome coronavirus 2] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7L4Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7L4Z 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=7l4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l4z OCA], [https://pdbe.org/7l4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l4z RCSB], [https://www.ebi.ac.uk/pdbsum/7l4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l4z 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]] 3.96Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=DTY:D-TYROSINE'>DTY</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</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=7l4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l4z OCA], [https://pdbe.org/7l4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l4z RCSB], [https://www.ebi.ac.uk/pdbsum/7l4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l4z 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 ==
		+	The COVID-19 pandemic, caused by SARS-CoV-2, has led to substantial morbidity, mortality, and disruption globally. Cellular entry of SARS-CoV-2 is mediated by the viral spike protein, and affinity ligands to this surface protein have the potential for applications as antivirals and diagnostic reagents. Here, we describe the affinity selection of cyclic peptide ligands to the SARS-CoV-2 spike protein receptor binding domain (RBD) from three distinct libraries (in excess of a trillion molecules each) by mRNA display. We identified six high affinity molecules with dissociation constants (K (D)) in the nanomolar range (15-550 nM) to the RBD. The highest affinity ligand could be used as an affinity reagent to detect the spike protein in solution by ELISA, and the cocrystal structure of this molecule bound to the RBD demonstrated that it binds to a cryptic binding site, displacing a beta-strand near the C-terminus. Our findings provide key mechanistic insight into the binding of peptide ligands to the SARS-CoV-2 spike RBD, and the ligands discovered in this work may find future use as reagents for diagnostic applications.
		+
		+	Discovery of Cyclic Peptide Ligands to the SARS-CoV-2 Spike Protein Using mRNA Display.,Norman A, Franck C, Christie M, Hawkins PME, Patel K, Ashhurst AS, Aggarwal A, Low JKK, Siddiquee R, Ashley CL, Steain M, Triccas JA, Turville S, Mackay JP, Passioura T, Payne RJ ACS Cent Sci. 2021 Jun 23;7(6):1001-1008. doi: 10.1021/acscentsci.0c01708. Epub , 2021 May 27. PMID:34230894<ref>PMID:34230894</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7l4z" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Severe acute respiratory syndrome coronavirus 2]]
		+	[[Category: Synthetic construct]]
		+	[[Category: Christie M]]
		+	[[Category: Mackay JP]]
		+	[[Category: Passioura T]]
		+	[[Category: Payne RJ]]

OCA at 03:33, 2 July 2021

2021-07-02T03:33:53Z

←Older revision		Revision as of 03:33, 2 July 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7l4z ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7l4z' size='340' side='right'caption='[[7l4z]]' 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=7l4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l4z OCA], [https://pdbe.org/7l4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l4z RCSB], [https://www.ebi.ac.uk/pdbsum/7l4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l4z ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA: Protected "7l4z" [edit=sysop:move=sysop]

2020-12-30T05:30:52Z

Protected "7l4z" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:30, 30 December 2020

OCA: New page: '''Unreleased structure''' The entry 7l4z is ON HOLD Authors: Description: Category: Unreleased Structures

2020-12-30T05:30:51Z

New page: '''Unreleased structure''' The entry 7l4z is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7l4z is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7l4z - Revision history

OCA at 15:37, 18 October 2023

OCA at 03:33, 2 July 2021

OCA: Protected "7l4z" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7l4z is ON HOLD Authors: Description: Category: Unreleased Structures