› 8zhj

Electron Microscopy
8.45Å resolution

SARS-CoV-2 spike trimer (6P) in complex with three H18 Fabs, head-to-head aggregate (C1 symmetry)

Released:
DOI: 10.2210/pdb8zhj/pdb
PDB entry 8zhj coloured by chain, front view.
PDB entry 8zhj coloured by chain, side view.
PDB entry 8zhj coloured by chain, top view.
Source organisms:
Primary publication:
Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein and potentially drive the genesis of Omicron variants.
Yan Q, Gao X, Liu B, Hou R, He P, Ma Y, Zhang Y, Zhang Y, Li Z, Chen Q, Wang J, Huang X, Liang H, Zheng H, Yao Y, Chen X, Niu X, He J, Chen L, Zhao J, Xiong X
Nat Commun 15 7585 (2024)
PMID: 39217172
Related structures: EMD-60105

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-497164 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
Fibritin C-terminal domain-containing protein; Spike glycoprotein Chains: A, B, C, G, H, I
Molecule details ›
Chains: A, B, C, G, H, I
Length: 1278 amino acids
Theoretical weight: 141.25 KDa
Source organisms: Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 11-1208; Coverage: 95%)
  • Canonical: A0A346FJN8 (Residues: 458-484; Coverage: 6%)
Gene names: 2, EcT6_00157, S, wac
Sequence domains:
Light chain of H18 Fab Chains: D, F, K, L, O, Q
Molecule details ›
Chains: D, F, K, L, O, Q
Length: 243 amino acids
Theoretical weight: 25.77 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Heavy chain of H18 Fab Chains: E, J, M, N, P, R
Molecule details ›
Chains: E, J, M, N, P, R
Length: 243 amino acids
Theoretical weight: 25.87 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand NAG 66 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 8.45Å
Relevant EMDB volumes: EMD-60105
Expression system: Homo sapiens

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