› 8bgg

Electron Microscopy
6.04Å resolution

Cryo-EM structure of SARS-CoV-2 spike (Omicron BA.1 variant) in complex with nanobody W25 (map 5, focus refinement on RBD, W25 and adjacent NTD)

Released:
DOI: 10.2210/pdb8bgg/pdb
PDB entry 8bgg coloured by chain, front view.
PDB entry 8bgg coloured by chain, side view.
PDB entry 8bgg coloured by chain, top view.
Source organisms:
Entry authors: Modhiran N, Lauer S, Spahn CMT, Watterson D, Schwefel D
Related structures: EMD-16030

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-272965 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (4 distinct):
Spike glycoprotein Chains: B, C
Molecule details ›
Chains: B, C
Length: 1205 amino acids
Theoretical weight: 133.91 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
Nanobody W25 Chain: Y
Molecule details ›
Chain: Y
Length: 167 amino acids
Theoretical weight: 17.83 KDa
Source organism: Vicugna pacos
Expression system: Escherichia coli

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
1 bound ligand:
Ligand NAG 5 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 6.04Å
Relevant EMDB volumes: EMD-16030
Expression systems:
  • Homo sapiens
  • Escherichia coli

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