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Structure paper

TitleStructural diversity of the SARS-CoV-2 Omicron spike.
Journal, issue, pagesMol Cell, Vol. 82, Issue 11, Page 2050-22068.e6, Year 2022
Publish dateJun 2, 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 / Amanda Eaton / David C Montefiori / 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 linksMol Cell / PubMed:35447081 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.15 - 4.07 Å
Structure data

EMDB-25846, PDB-7tei:
SARS-CoV-2 Omicron 1-RBD up Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron)
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-25865, PDB-7tf8:
SARS-CoV-2 Omicron 3-RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron)
Method: EM (single particle) / Resolution: 3.36 Å

EMDB-25904: CryoEM map of SARS-CoV-2 S protein in complex with Receptor Binding Domain antibody DH1042
PDB-7tht: CryoEM structure of SARS-CoV-2 S protein in complex with Receptor Binding Domain antibody DH1042
Method: EM (single particle) / Resolution: 3.42 Å

EMDB-25983, PDB-7tl1:
SARS-CoV-2 Omicron 3-RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron)
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-25984, PDB-7tl9:
SARS-CoV-2 Omicron 1-RBD up Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron)
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-25985, PDB-7tla:
Down-state locked rS2d SARS-CoV-2 spike ectodomain in the RBD-down conformation, State 1
Method: EM (single particle) / Resolution: 3.13 Å

EMDB-25987, PDB-7tlc:
Down-state locked, S2 stabilized rS2d-HexaPro SARS-CoV-2 spike ectodomain in the RBD-down conformation, State 1
Method: EM (single particle) / Resolution: 2.83 Å

EMDB-25988, PDB-7tld:
Down-state locked, S2 stabilized rS2d-HexaPro SARS-CoV-2 spike ectodomain in the RBD-down conformation, State 2
Method: EM (single particle) / Resolution: 2.89 Å

EMDB-26038, PDB-7tou:
Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; consensus state D1
Method: EM (single particle) / Resolution: 3.24 Å

EMDB-26039, PDB-7tov:
Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; consensus state D2
Method: EM (single particle) / Resolution: 3.16 Å

EMDB-26040, PDB-7tox:
Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; Subclassification D5 state
Method: EM (single particle) / Resolution: 3.62 Å

EMDB-26041, PDB-7toy:
Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; Subclassification D6 state
Method: EM (single particle) / Resolution: 3.53 Å

EMDB-26042, PDB-7toz:
Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; Subclassification D7 state
Method: EM (single particle) / Resolution: 4.07 Å

EMDB-26043, PDB-7tp0:
Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; Subclassification D8 state
Method: EM (single particle) / Resolution: 3.57 Å

EMDB-26045, PDB-7tp1:
Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; Subclassification D9 state
Method: EM (single particle) / Resolution: 3.81 Å

EMDB-26046, PDB-7tp2:
Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; Subclassification D10 state
Method: EM (single particle) / Resolution: 3.72 Å

EMDB-26047, PDB-7tp7:
Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D11 state
Method: EM (single particle) / Resolution: 3.48 Å

EMDB-26048, PDB-7tp8:
Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D12 state
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-26049, PDB-7tp9:
Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D13 state
Method: EM (single particle) / Resolution: 3.48 Å

EMDB-26050, PDB-7tpa:
Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D14 state
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-26051, PDB-7tpc:
Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D15 state
Method: EM (single particle) / Resolution: 3.91 Å

EMDB-26052, PDB-7tpe:
Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D16 state
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-26053, PDB-7tpf:
Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D17 state
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-26055, PDB-7tph:
Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 2-RBD-up conformation - D3
Method: EM (single particle) / Resolution: 3.58 Å

EMDB-26059, PDB-7tpl:
Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the M1 conformation, D4
Method: EM (single particle) / Resolution: 3.87 Å

PDB-7tow:
Antibody DH1058 Fab fragment bound to SARS-CoV-2 fusion peptide
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

Chemicals

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

ChemComp-CA:
Unknown entry

ChemComp-PO4:
PHOSPHATE ION

ChemComp-HOH:
WATER

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
KeywordsVIRAL PROTEIN / Omicron Spike protein / SARS-CoV-2 / variant of concern / 1-up / 3-down / VIRAL PROTEIN/IMMUNE SYSTEM / RBD antibody / DH1042 / SARS / COVID-19 / SARS-CoV-2 2P S ectodomain / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex / Spike / Fusion Protein / SARS-CoV-2 Spike Protein Trimer / IMMUNE SYSTEM/Viral Protein / Antibody / Fab fragment / IMMUNE SYSTEM-Viral Protein complex

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