OCA at 03:53, 8 September 2022

2022-09-08T03:53:48Z

←Older revision		Revision as of 03:53, 8 September 2022
Line 1:		Line 1:

-	====	+	==Structure of RBD directed antibody DH1042 in complex with SARS-CoV-2 spike: Local refinement of RBD-Fab interface==
-	<StructureSection load='7the' size='340' side='right'caption='[[7the]]' scene=''>	+	<StructureSection load='7the' size='340' side='right'caption='[[7the]], [[Resolution\|resolution]] 3.87Å' 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'>[[7the]] 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=7THE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7THE 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=7the FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7the OCA], [https://pdbe.org/7the PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7the RCSB], [https://www.ebi.ac.uk/pdbsum/7the PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7the ProSAT]</span></td></tr>	+	</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=7the FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7the OCA], [https://pdbe.org/7the PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7the RCSB], [https://www.ebi.ac.uk/pdbsum/7the PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7the 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 ==
		+	Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. Spike conformation plays an essential role in SARS-CoV-2 evolution via changes in receptor-binding domain (RBD) and neutralizing antibody epitope presentation, affecting virus transmissibility and immune evasion. Here, we determine cryo-EM structures of the Omicron and Delta spikes to understand the conformational impacts of mutations in each. The Omicron spike structure revealed an unusually tightly packed RBD organization with long range impacts that were not observed in the Delta spike. Binding and crystallography revealed increased flexibility at the functionally critical fusion peptide site in the Omicron spike. These results reveal a highly evolved Omicron spike architecture with possible impacts on its high levels of immune evasion and transmissibility.
		+
		+	Structural diversity of the SARS-CoV-2 Omicron spike.,Gobeil SM, Henderson R, Stalls V, Janowska K, Huang X, May A, Speakman M, Beaudoin E, Manne K, Li D, Parks R, Barr M, Deyton M, Martin M, Mansouri K, Edwards RJ, Eaton A, Montefiori DC, Sempowski GD, Saunders KO, Wiehe K, Williams W, Korber B, Haynes BF, Acharya P Mol Cell. 2022 Jun 2;82(11):2050-2068.e6. doi: 10.1016/j.molcel.2022.03.028. Epub, 2022 Mar 25. PMID:35447081<ref>PMID:35447081</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7the" style="background-color:#fffaf0;"></div>
		+	== 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: Acharya P]]
		+	[[Category: Manne K]]
		+	[[Category: May AJ]]

OCA at 10:18, 16 February 2022

2022-02-16T10:18:34Z

←Older revision		Revision as of 10:18, 16 February 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7the ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7the' size='340' side='right'caption='[[7the]]' scene=''>
-	~~Authors~~: ~~May, A~~.J.~~, Manne, K~~.~~, Acharya, P~~.	+	== 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~~: ~~Structure of RBD directed antibody DH1042 in complex with SARS-CoV-2 spike~~: ~~Local refinement of RBD~~-~~Fab interface~~	+	</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=7the FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7the OCA], [https://pdbe.org/7the PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7the RCSB], [https://www.ebi.ac.uk/pdbsum/7the PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7the ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: ~~Acharya~~, P]]	+	__TOC__
-	[[Category: ~~Manne, K~~]]	+	</StructureSection>
-	[[Category: ~~May, A.J~~]]	+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

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

2022-01-19T06:02:42Z

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

←Older revision

Revision as of 06:02, 19 January 2022

OCA: New page: '''Unreleased structure''' The entry 7the is ON HOLD Authors: May, A.J., Manne, K., Acharya, P. Description: Structure of RBD directed antibody DH1042 in complex with SARS-CoV-2 spike:...

2022-01-19T06:02:40Z

New page: '''Unreleased structure''' The entry 7the is ON HOLD Authors: May, A.J., Manne, K., Acharya, P. Description: Structure of RBD directed antibody DH1042 in complex with SARS-CoV-2 spike:...

New page

'''Unreleased structure'''

The entry 7the is ON HOLD

Authors: May, A.J., Manne, K., Acharya, P.

Description: Structure of RBD directed antibody DH1042 in complex with SARS-CoV-2 spike: Local refinement of RBD-Fab interface
[[Category: Unreleased Structures]]
[[Category: Acharya, P]]
[[Category: Manne, K]]
[[Category: May, A.J]]

7the - Revision history

OCA at 03:53, 8 September 2022

OCA at 10:18, 16 February 2022

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

OCA: New page: '''Unreleased structure''' The entry 7the is ON HOLD Authors: May, A.J., Manne, K., Acharya, P. Description: Structure of RBD directed antibody DH1042 in complex with SARS-CoV-2 spike:...