› 8zbz

Electron Microscopy
4.71Å resolution

SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with 3 D1F6 Fabs (1 RBD up)

Released:
DOI: 10.2210/pdb8zbz/pdb
PDB entry 8zbz coloured by chain, front view.
PDB entry 8zbz coloured by chain, side view.
PDB entry 8zbz coloured by chain, top view.
Source organisms:
Primary publication:
An unconventional VH1-2 antibody tolerates escape mutations and shows an antigenic hotspot on SARS-CoV-2 spike.
Liu B, Niu X, Deng Y, Zhang Z, Wang Y, Gao X, Liang H, Li Z, Wang Q, Cheng Y, Chen Q, Huang S, Pan Y, Su M, Lin X, Niu C, Chen Y, Yang W, Zhang Y, Yan Q, He J, Zhao J, Chen L, Xiong X
Cell Rep 43 114265 (2024)
PMID: 38805396
Related structures: EMD-39917

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero nonamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-244394 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (5 distinct):
Spike glycoprotein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 1240 amino acids
Theoretical weight: 137.89 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 14-1211; Coverage: 95%)
Gene names: 2, S
Sequence domains:
Light chain of D1F6 Fab Chains: D, M, N
Molecule details ›
Chains: D, M, N
Length: 223 amino acids
Theoretical weight: 23.62 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Heavy chain of D1F6 Fab Chains: E, Q, R
Molecule details ›
Chains: E, Q, R
Length: 230 amino acids
Theoretical weight: 24.75 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
1 bound ligand:
Ligand NAG 24 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.71Å
Relevant EMDB volumes: EMD-39917
Expression system: Homo sapiens

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