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CryoEM structure of inactivated-form DNA-PK (Complex IV)

Electron Microscopy
4.1Å resolution
PDB entry 7k1k coloured by chain, front view.
PDB entry 7k1k coloured by chain, side view.
PDB entry 7k1k coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero heptamer (preferred)
Entry contents: 3 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: DNA-dependent protein kinase complex and DNA
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Multimeric state: hetero heptamer
Accessible surface area: 238330.58 Å2
Buried surface area: 27855.35 Å2
Dissociation area: 4,350.92 Å2
Dissociation energy (ΔGdiss): 10.4 kcal/mol
Dissociation entropy (TΔSdiss): 43.24 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-121421

Macromolecules

DNA-dependent protein kinase catalytic subunit
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
Pfam:
InterPro:
DNA-dependent protein kinase catalytic subunit in PDB entry 7k1k, assembly 1, front view.
DNA-dependent protein kinase catalytic subunit in PDB entry 7k1k, assembly 1, side view.
DNA-dependent protein kinase catalytic subunit in PDB entry 7k1k, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P78527  
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X-ray repair cross-complementing protein 6
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
Pfam:
InterPro:
X-ray repair cross-complementing protein 6 in PDB entry 7k1k, assembly 1, front view.
X-ray repair cross-complementing protein 6 in PDB entry 7k1k, assembly 1, side view.
X-ray repair cross-complementing protein 6 in PDB entry 7k1k, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P12956  
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X-ray repair cross-complementing protein 5
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
Pfam:
InterPro:
X-ray repair cross-complementing protein 5 in PDB entry 7k1k, assembly 1, front view.
X-ray repair cross-complementing protein 5 in PDB entry 7k1k, assembly 1, side view.
X-ray repair cross-complementing protein 5 in PDB entry 7k1k, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P13010  
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DNA chains D, F
Name: 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')
Representative chains: D, F
Length: 24 nucleotides
Theoretical weight: 7.31 KDa
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') in PDB entry 7k1k, assembly 1, front view.
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') in PDB entry 7k1k, assembly 1, side view.
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') in PDB entry 7k1k, assembly 1, top view.
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DNA chains E, G
Name: DNA (5'-D(*AP*AP*GP*CP*AP*GP*TP*AP*GP*AP*GP*CP*A)-3')
Representative chains: E, G
Length: 16 nucleotides
Theoretical weight: 4.96 KDa
DNA (5'-D(*AP*AP*GP*CP*AP*GP*TP*AP*GP*AP*GP*CP*A)-3') in PDB entry 7k1k, assembly 1, front view.
DNA (5'-D(*AP*AP*GP*CP*AP*GP*TP*AP*GP*AP*GP*CP*A)-3') in PDB entry 7k1k, assembly 1, side view.
DNA (5'-D(*AP*AP*GP*CP*AP*GP*TP*AP*GP*AP*GP*CP*A)-3') in PDB entry 7k1k, assembly 1, top view.
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