› 8zc6

Electron Microscopy
6.85Å resolution

SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with D1F6 Fab, head-to-head aggregate

Released:
DOI: 10.2210/pdb8zc6/pdb
PDB entry 8zc6 coloured by chain, front view.
PDB entry 8zc6 coloured by chain, side view.
PDB entry 8zc6 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-39924

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-244794 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Spike glycoprotein Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 1238 amino acids
Theoretical weight: 137.62 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 14-1211; Coverage: 94%)
Gene names: 2, S
Sequence domains:
Light chain of D1F6 Fab Chains: G, I, K, L, M, N
Molecule details ›
Chains: G, I, K, L, 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: H, J, O, P, Q, R
Molecule details ›
Chains: H, J, O, P, Q, R
Length: 230 amino acids
Theoretical weight: 24.75 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens

Ligands and Environments

1 bound ligand:
Ligand NAG 20 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 6.85Å
Relevant EMDB volumes: EMD-39924
Expression system: Homo sapiens

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