7r1b
From Proteopedia
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==Mink Variant SARS-CoV-2 Spike with 1 Erect RBD== | ==Mink Variant SARS-CoV-2 Spike with 1 Erect RBD== | ||
| - | <StructureSection load='7r1b' size='340' side='right'caption='[[7r1b]]' scene=''> | + | <StructureSection load='7r1b' size='340' side='right'caption='[[7r1b]], [[Resolution|resolution]] 2.80Å' 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=7R1B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7R1B FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7r1b]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7R1B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7R1B 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=7r1b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7r1b OCA], [https://pdbe.org/7r1b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7r1b RCSB], [https://www.ebi.ac.uk/pdbsum/7r1b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7r1b 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=7r1b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7r1b OCA], [https://pdbe.org/7r1b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7r1b RCSB], [https://www.ebi.ac.uk/pdbsum/7r1b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7r1b 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 == | ||
| + | Recently emerged variants of SARS-CoV-2 contain in their surface spike glycoproteins multiple substitutions associated with increased transmission and resistance to neutralising antibodies. We have examined the structure and receptor binding properties of spike proteins from the B.1.1.7 (Alpha) and B.1.351 (Beta) variants to better understand the evolution of the virus in humans. Spikes of both variants have the same mutation, N501Y, in the receptor-binding domains. This substitution confers tighter ACE2 binding, dependent on the common earlier substitution, D614G. Each variant spike has acquired other key changes in structure that likely impact virus pathogenesis. The spike from the Alpha variant is more stable against disruption upon binding ACE2 receptor than all other spikes studied. This feature is linked to the acquisition of a more basic substitution at the S1-S2 furin site (also observed for the variants of concern Delta, Kappa, and Omicron) which allows for near-complete cleavage. In the Beta variant spike, the presence of a new substitution, K417N (also observed in the Omicron variant), in combination with the D614G, stabilises a more open spike trimer, a conformation required for receptor binding. Our observations suggest ways these viruses have evolved to achieve greater transmissibility in humans. | ||
| + | |||
| + | Evolution of the SARS-CoV-2 spike protein in the human host.,Wrobel AG, Benton DJ, Roustan C, Borg A, Hussain S, Martin SR, Rosenthal PB, Skehel JJ, Gamblin SJ Nat Commun. 2022 Mar 4;13(1):1178. doi: 10.1038/s41467-022-28768-w. PMID:35246509<ref>PMID:35246509</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7r1b" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Benton | + | [[Category: Benton, D J]] |
| - | [[Category: Gamblin | + | [[Category: Gamblin, S J]] |
| - | [[Category: Wrobel | + | [[Category: Wrobel, A G]] |
| + | [[Category: Sars-cov-2]] | ||
| + | [[Category: Spike]] | ||
| + | [[Category: Viral protein]] | ||
Revision as of 07:22, 16 March 2022
Mink Variant SARS-CoV-2 Spike with 1 Erect RBD
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