› 8hpv

Electron Microscopy
2.65Å resolution

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

Released:
DOI: 10.2210/pdb8hpv/pdb
PDB entry 8hpv coloured by chain, front view.
PDB entry 8hpv coloured by chain, side view.
PDB entry 8hpv 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
OpenAccess logo Cell Discov 9 79 (2023)
PMID: 37507370
Related structures: EMD-34945

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-279759 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (6 distinct):
Spike glycoprotein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 1134 amino acids
Theoretical weight: 125.61 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 L5.34 Chains: E, M, R
Molecule details ›
Chains: E, M, R
Length: 225 amino acids
Theoretical weight: 23.72 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
fab L5.34 Chains: F, N, S
Molecule details ›
Chains: F, N, S
Length: 216 amino acids
Theoretical weight: 23.38 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 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

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.65Å
Relevant EMDB volumes: EMD-34945
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)