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TitleStructural diversity of the SARS-CoV-2 Omicron spike.
Journal, issue, pagesbioRxiv, Year 2022
Publish dateJan 26, 2022
AuthorsSophie M-C Gobeil / Rory Henderson / Victoria Stalls / Katarzyna Janowska / Xiao Huang / Aaron May / Micah Speakman / Esther Beaudoin / Kartik Manne / Dapeng Li / Rob Parks / Maggie Barr / Margaret Deyton / Mitchell Martin / Katayoun Mansouri / Robert J Edwards / Gregory D Sempowski / Kevin O Saunders / Kevin Wiehe / Wilton Williams / Bette Korber / Barton F Haynes / Priyamvada Acharya
PubMed AbstractAided 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 ...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.
External linksbioRxiv / PubMed:35118469 / PubMed Central
MethodsEM (single particle)
Resolution3.06 - 3.96 Å
Structure data

25880

7tge

EMDB-25880, PDB-7tge:
SARS-CoV-2 Omicron 1-RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron)
Method: EM (single particle) / Resolution: 3.68 Å

25893

7the

EMDB-25893, PDB-7the:
Structure of RBD directed antibody DH1042 in complex with SARS-CoV-2 spike: Local refinement of RBD-Fab interface
Method: EM (single particle) / Resolution: 3.87 Å

25986

7tlb

EMDB-25986, PDB-7tlb:
Down-state locked rS2d SARS-CoV-2 spike ectodomain in the RBD-down conformation, State 2
Method: EM (single particle) / Resolution: 3.06 Å

EMDB-26600: SARS-CoV-2 Omicron-BA.1 2-RBD up Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron-BA.1)
Method: EM (single particle) / Resolution: 3.96 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
KeywordsVIRAL PROTEIN / Omicron Spike protein / SARS-CoV-2 / variant of concern / 1-down / VIRAL PROTEIN/IMMUNE SYSTEM / RBD / Fab / VIRAL PROTEIN-IMMUNE SYSTEM complex / Spike / Fusion Protein

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