› 8dzi

Electron Microscopy
3.5Å resolution

Structure of SARS-CoV-2 Omicron BA.1.1.529 Spike trimer with one RBD down in complex with the Fab fragment of human neutralizing antibody MB.02

Released:
DOI: 10.2210/pdb8dzi/pdb
PDB entry 8dzi coloured by chain, front view.
PDB entry 8dzi coloured by chain, side view.
PDB entry 8dzi coloured by chain, top view.
Source organisms:
Primary publication:
Function and Cryo-EM structures of broadly potent bispecific antibodies against multiple SARS-CoV-2 Omicron sublineages.
Ren P, Hu Y, Peng L, Yang L, Suzuki K, Fang Z, Bai M, Zhou L, Feng Y, Zou Y, Xiong Y, Chen S
OpenAccess logo Signal Transduct Target Ther 8 281 (2023)
PMID: 37518189
Related structures: EMD-27799

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero nonamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-276130 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
Spike glycoprotein Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 1285 amino acids
Theoretical weight: 142.59 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
antibody MB.02 heavy chain Chains: B, G, H
Molecule details ›
Chains: B, G, H
Length: 118 amino acids
Theoretical weight: 12.97 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
antibody MB.02 light chain Chains: D, F, L

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand NAG 23 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.5Å
Relevant EMDB volumes: EMD-27799
Expression system: Homo sapiens

Quick links

Citations

2 review citations

Broadly neutralizing antibodies against COVID-19.
Zhou et al. (2023)
1 more

1 mention without citation

Distinct Conformations of SARS-CoV-2 Omicron Spike Protein and Its Interaction with ACE2 and Antibody.
Lee et al. (2023)