› 8hp9

Electron Microscopy
2.75Å resolution

Cryo-EM structure of SARS-CoV-2 Omicron BA.2 S-trimer in complex with fab L4.65 and L5.34

Released:
DOI: 10.2210/pdb8hp9/pdb
PDB entry 8hp9 coloured by chain, front view.
PDB entry 8hp9 coloured by chain, side view.
PDB entry 8hp9 coloured by chain, top view.
Source organisms:
Primary publication:
Dosing interval regimen shapes potency and breadth of antibody repertoire after vaccination of SARS-CoV-2 RBD protein subunit vaccine.
Guo S, Zheng Y, Gao Z, Duan M, Liu S, Du P, Xu X, Xu K, Zhao X, Chai Y, Wang P, Zhao Q, Gao GF, Dai L
Cell Discov 9 79 (2023)
PMID: 37507370
Related structures: EMD-34928

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero pentadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-239375 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Spike glycoprotein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 1131 amino acids
Theoretical weight: 125.56 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 14-1147; Coverage: 90%)
Gene names: 2, S
Sequence domains:
fab L4.65 Chains: J, L, Q
Molecule details ›
Chains: J, L, Q
Length: 215 amino acids
Theoretical weight: 23.56 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
fab L4.65 Chains: H, I, P
Molecule details ›
Chains: H, I, P
Length: 231 amino acids
Theoretical weight: 24.95 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
fab L5.34 Chains: E, K, M
Molecule details ›
Chains: E, K, M
Length: 224 amino acids
Theoretical weight: 23.59 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
fab L5.34 Chains: F, N, O
Molecule details ›
Chains: F, N, O
Length: 216 amino acids
Theoretical weight: 23.38 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens

Ligands and Environments

1 bound ligand:
Ligand NAG 32 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.75Å
Relevant EMDB volumes: EMD-34928
Expression system: Homo sapiens

Quick links

Citations

1 citations in other articles

Defining a de novo non-RBM antibody as RBD-8 and its synergistic rescue of immune-evaded antibodies to neutralize Omicron SARS-CoV-2.
Rao et al. (2023)