› 7y9s

Electron Microscopy
3Å resolution

Cryo-EM structure of apo SARS-CoV-2 Omicron spike protein (S-2P-GSAS)

Released:
DOI: 10.2210/pdb7y9s/pdb
PDB entry 7y9s coloured by chain, front view.
PDB entry 7y9s coloured by chain, side view.
PDB entry 7y9s coloured by chain, top view.
Source organism: Severe acute respiratory syndrome coronavirus 2
Primary publication:
Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape.
Zhao Z, Zhou J, Tian M, Huang M, Liu S, Xie Y, Han P, Bai C, Han P, Zheng A, Fu L, Gao Y, Peng Q, Li Y, Chai Y, Zhang Z, Zhao X, Song H, Qi J, Wang Q, Wang P, Gao GF
OpenAccess logo Nat Commun 13 4958 (2022)
PMID: 36002453
Related structures: EMD-33690

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-144650 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Spike glycoprotein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 1249 amino acids
Theoretical weight: 138.84 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 15-210, 211-211, 215-1208; Coverage: 94%)
Gene names: 2, S
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand NAG 21 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3Å
Relevant EMDB volumes: EMD-33690
Expression system: Homo sapiens

Quick links

Citations

8 review citations

Defending against SARS-CoV-2: The T cell perspective.
Almendro-Vázquez et al. (2023)
7 more

3 mentions without citation

Dual-Affinity Graphene Sheets for High-Resolution Cryo-Electron Microscopy.
Cheng et al. (2023)
2 more