› 8hcb

Electron Microscopy
4.18Å resolution

SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 3 YB13-292 Fabs (2 RBD up)

Released:
DOI: 10.2210/pdb8hcb/pdb
PDB entry 8hcb coloured by chain, front view.
PDB entry 8hcb coloured by chain, side view.
PDB entry 8hcb coloured by chain, top view.
Source organisms:
Primary publication:
Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants.
Yu H, Liu B, Zhang Y, Gao X, Wang Q, Xiang H, Peng X, Xie C, Wang Y, Hu P, Shi J, Shi Q, Zheng P, Feng C, Tang G, Liu X, Guo L, Lin X, Li J, Liu C, Huang Y, Yang N, Chen Q, Li Z, Su M, Yan Q, Pei R, Chen X, Liu L, Hu F, Liang D, Ke B, Ke C, Li F, He J, Wang M, Chen L, Xiong X, Tang X
OpenAccess logo Nat Commun 14 1058 (2023)
PMID: 36828833
Related structures: EMD-34658

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero nonamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-225449 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
Spike glycoprotein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 1240 amino acids
Theoretical weight: 138.04 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 14-210, 211-211, 215-1211; Coverage: 94%)
Gene names: 2, S
Sequence domains:
Light chain of YB13-292 Fab Chains: E, G, L
Molecule details ›
Chains: E, G, L
Length: 219 amino acids
Theoretical weight: 23.98 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Heavy chain of YB13-292 Fab Chains: D, F, H
Molecule details ›
Chains: D, F, H
Length: 238 amino acids
Theoretical weight: 25.28 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand NAG 30 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.18Å
Relevant EMDB volumes: EMD-34658
Expression system: Homo sapiens

Quick links

Citations

1 citations in other articles

DNA Framework Programmed Conformational Reconstruction of Antibody Complementary Determining Region.
Zhou et al. (2023)