› 8hc4

Electron Microscopy
3.54Å resolution

SARS-CoV-2 wildtype spike trimer (6P) in complex with 3 YB9-258 Fabs and 3 R1-32 Fabs (3 RBD up)

Released:
DOI: 10.2210/pdb8hc4/pdb
PDB entry 8hc4 coloured by chain, front view.
PDB entry 8hc4 coloured by chain, side view.
PDB entry 8hc4 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-34651

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-225446 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (6 distinct):
Spike glycoprotein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 1208 amino acids
Theoretical weight: 133.78 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 1-1208; Coverage: 95%)
Gene names: 2, S
Sequence domains:
Heavy chain of R1-32 Fab Chains: D, K, N
Molecule details ›
Chains: D, K, N
Length: 228 amino acids
Theoretical weight: 23.84 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Light chain of R1-32 Fab Chains: E, M, O
Molecule details ›
Chains: E, M, O
Length: 214 amino acids
Theoretical weight: 22.38 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Heavy chain of YB9-258 Chains: F, G, H
Molecule details ›
Chains: F, G, H
Length: 220 amino acids
Theoretical weight: 23.13 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Light chain of YB9-258 Fab Chains: I, J, L
Molecule details ›
Chains: I, J, L
Length: 215 amino acids
Theoretical weight: 23.18 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: 3.54Å
Relevant EMDB volumes: EMD-34651
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)