› 8jva

Electron Microscopy
2.81Å resolution

Cryo-EM structure of the N-terminal domain of Omicron BA.1 in complex with nanobody N235 and S2L20 Fab

Released:
DOI: 10.2210/pdb8jva/pdb
PDB entry 8jva coloured by chain, front view.
PDB entry 8jva coloured by chain, side view.
PDB entry 8jva coloured by chain, top view.
Source organisms:
Primary publication:
Enhanced potency of an IgM-like nanobody targeting conserved epitope in SARS-CoV-2 spike N-terminal domain.
Liu B, Liu H, Han P, Wang X, Wang C, Yan X, Lei W, Xu K, Zhou J, Qi J, Fan R, Wu G, Tian WX, Gao GF, Wang Q
Signal Transduct Target Ther 9 131 (2024)
PMID: 38740785
Related structures: EMD-36672

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-272944 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
nanobody N235 Chain: D
Molecule details ›
Chain: D
Length: 126 amino acids
Theoretical weight: 13.97 KDa
Source organism: Vicugna pacos
Expression system: Homo sapiens
S2L20 light chain Chain: A
Molecule details ›
Chain: A
Length: 236 amino acids
Theoretical weight: 26.02 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
S2L20 heavy chain Chain: B
Molecule details ›
Chain: B
Length: 473 amino acids
Theoretical weight: 52.04 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Spike protein S1 Chain: F
Molecule details ›
Chain: F
Length: 300 amino acids
Theoretical weight: 34.08 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 1-210, 211-211, 215-303; Coverage: 22%)
Gene names: 2, S
Sequence domains: Betacoronavirus-like spike glycoprotein S1, N-terminal

Ligands and Environments

1 bound ligand:
Ligand NAG 5 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.81Å
Relevant EMDB volumes: EMD-36672
Expression system: Homo sapiens

Quick links