› 6xey

Electron Microscopy
3.25Å resolution

Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to Fab 2-4

Released:
DOI: 10.2210/pdb6xey/pdb
PDB entry 6xey coloured by chain, front view.
PDB entry 6xey coloured by chain, side view.
PDB entry 6xey coloured by chain, top view.
Source organisms:
Primary publication:
Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike.
Liu L, Wang P, Nair MS, Yu J, Rapp M, Wang Q, Luo Y, Chan JF, Sahi V, Figueroa A, Guo XV, Cerutti G, Bimela J, Gorman J, Zhou T, Chen Z, Yuen KY, Kwong PD, Sodroski JG, Yin MT, Sheng Z, Huang Y, Shapiro L, Ho DD
Nature 584 450-456 (2020)
PMID: 32698192
Related structures: EMD-22156

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-207480 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (6 distinct):
Spike glycoprotein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 1288 amino acids
Theoretical weight: 142.4 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:
2-4 Heavy Chain Chains: F, H, J
Molecule details ›
Chains: F, H, J
Length: 122 amino acids
Theoretical weight: 13.71 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Ig-like domain-containing protein Chains: G, K, L
Molecule details ›
Chains: G, K, L
Length: 110 amino acids
Theoretical weight: 11.4 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: A0A5C2GJG2 (Residues: 1-110; Coverage: 100%)
Sequence domains: Immunoglobulin V-set domain

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
1 bound ligand:
Ligand NAG 36 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.25Å
Relevant EMDB volumes: EMD-22156
Expression system: Homo sapiens

Quick links

Citations

166 review citations

SARS-CoV-2 vaccines in development.
Krammer F. (2020)
165 more

45 mentions without citation

The SARS-CoV-2 Spike Glycoprotein as a Drug and Vaccine Target: Structural Insights into Its Complexes with ACE2 and Antibodies.
Papageorgiou et al. (2020)
44 more