7tgw

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==Omicron spike at 3.0 A (open form)==
==Omicron spike at 3.0 A (open form)==
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<StructureSection load='7tgw' size='340' side='right'caption='[[7tgw]]' scene=''>
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<StructureSection load='7tgw' size='340' side='right'caption='[[7tgw]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TGW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TGW FirstGlance]. <br>
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<table><tr><td colspan='2'>[[7tgw]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TGW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TGW FirstGlance]. <br>
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</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=7tgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tgw OCA], [https://pdbe.org/7tgw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tgw RCSB], [https://www.ebi.ac.uk/pdbsum/7tgw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tgw ProSAT]</span></td></tr>
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</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>
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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=7tgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tgw OCA], [https://pdbe.org/7tgw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tgw RCSB], [https://www.ebi.ac.uk/pdbsum/7tgw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tgw ProSAT]</span></td></tr>
</table>
</table>
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== Function ==
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[[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]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The omicron variant of SARS-CoV-2 has been spreading rapidly across the globe. The virus-surface spike protein plays a critical role in the cell entry and immune evasion of SARS-CoV-2. Here we determined the 3.0 A cryo-EM structure of the omicron spike protein ectodomain. In contrast to the original strain of SARS-CoV-2 where the receptor-binding domain (RBD) of the spike protein takes a mixture of open ("standing up") and closed ("lying down") conformations, the omicron spike molecules are predominantly in the open conformation, with one upright RBD ready for receptor binding. The open conformation of the omicron spike is stabilized by enhanced inter-domain and inter-subunit packing, which involves new mutations in the omicron strain. Moreover, the omicron spike has undergone extensive mutations in RBD regions where known neutralizing antibodies target, allowing the omicron variant to escape immune surveillance aimed at the original viral strain. The stable open conformation of the omicron spike sheds light on the cell entry and immune evasion mechanisms of the omicron variant.
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Cryo-EM structure of a SARS-CoV-2 omicron spike protein ectodomain.,Ye G, Liu B, Li F Nat Commun. 2022 Mar 3;13(1):1214. doi: 10.1038/s41467-022-28882-9. PMID:35241675<ref>PMID:35241675</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 7tgw" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Li F]]
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[[Category: Li, F]]
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[[Category: Liu B]]
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[[Category: Liu, B]]
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[[Category: Ye G]]
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[[Category: Ye, G]]
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[[Category: Omicron spike]]
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[[Category: Sars-cov-2]]
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[[Category: Viral protein]]

Revision as of 07:24, 16 March 2022

Omicron spike at 3.0 A (open form)

PDB ID 7tgw

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