› 7k0y

Electron Microscopy
3.7Å resolution

Cryo-EM structure of activated-form DNA-PK (complex VI)

Released:
DOI: 10.2210/pdb7k0y/pdb
PDB entry 7k0y coloured by chain, front view.
PDB entry 7k0y coloured by chain, side view.
PDB entry 7k0y coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of an activated DNA-PK and its implications for NHEJ.
Chen X, Xu X, Chen Y, Cheung JC, Wang H, Jiang J, de Val N, Fox T, Gellert M, Yang W
Mol Cell 81 801-810.e3 (2021)
PMID: 33385326
Related structures: EMD-22618

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero heptamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-121417 (preferred)
Entry contents:
3 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (5 distinct):
DNA-dependent protein kinase catalytic subunit Chain: A
Molecule details ›
Chain: A
Length: 4128 amino acids
Theoretical weight: 469.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P78527 (Residues: 1-4128; Coverage: 100%)
Gene names: HYRC, HYRC1, PRKDC
Sequence domains:
X-ray repair cross-complementing protein 6 Chain: B
Molecule details ›
Chain: B
Length: 609 amino acids
Theoretical weight: 69.95 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P12956 (Residues: 1-609; Coverage: 100%)
Gene names: G22P1, XRCC6
Sequence domains:
X-ray repair cross-complementing protein 5 Chain: C
Molecule details ›
Chain: C
Length: 732 amino acids
Theoretical weight: 82.81 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P13010 (Residues: 1-732; Coverage: 100%)
Gene names: G22P2, XRCC5
Sequence domains:
DNA (5'-D(*GP*CP*AP*TP*GP*CP*TP*CP*TP*AP*CP*TP*GP*CP*TP*TP*CP*GP*AP*TP*AP*TP*CP*G)-3') Chains: D, F
Molecule details ›
Chains: D, F
Length: 24 nucleotides
Theoretical weight: 7.31 KDa
DNA (5'-D(*AP*AP*GP*CP*AP*GP*TP*AP*GP*AP*GP*CP*A)-3') Chains: E, G
Molecule details ›
Chains: E, G
Length: 16 nucleotides
Theoretical weight: 4.96 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.7Å
Relevant EMDB volumes: EMD-22618
Expression system: Homo sapiens

Quick links

Citations

17 review citations

Function and Molecular Mechanism of the DNA Damage Response in Immunity and Cancer Immunotherapy.
Ye et al. (2021)
16 more

7 mentions without citation

Development and Evolution of DNA-Dependent Protein Kinase Inhibitors toward Cancer Therapy.
Matsumoto Y. (2022)
6 more