8bh3

Electron Microscopy
4.55Å resolution

Function and Biology Details

Reactions catalysed:
ATP + a protein = ADP + a phosphoprotein
(1a) ATP + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + diphosphate

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
PDBe Complex ID:
PDB-CPX-217216 (preferred)
Entry contents:
6 distinct polypeptide molecules
4 distinct DNA molecules
Macromolecules (10 distinct):
DNA-dependent protein kinase catalytic subunit Chains: A, S
Molecule details ›
Chains: A, S
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 Chains: B, T
Molecule details ›
Chains: B, T
Length: 609 amino acids
Theoretical weight: 69.95 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P12956 (Residues: 1-609; Coverage: 100%)
Gene names: G22P1, XRCC6
Sequence domains:
X-ray repair cross-complementing protein 5 Chains: C, L
Molecule details ›
Chains: C, L
Length: 732 amino acids
Theoretical weight: 82.81 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P13010 (Residues: 1-732; Coverage: 100%)
Gene names: G22P2, XRCC5
Sequence domains:
Protein PAXX Chains: D, M
Molecule details ›
Chains: D, M
Length: 204 amino acids
Theoretical weight: 21.66 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9BUH6 (Residues: 1-204; Coverage: 100%)
Gene names: C9orf142, PAXX, XLS
Sequence domains: PAXX, PAralog of XRCC4 and XLF, also called C9orf142
DNA repair protein XRCC4 Chains: G, H, P, Q
Molecule details ›
Chains: G, H, P, Q
Length: 336 amino acids
Theoretical weight: 38.34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q13426 (Residues: 1-336; Coverage: 100%)
Gene name: XRCC4
Sequence domains:
DNA ligase 4 Chains: I, R
Molecule details ›
Chains: I, R
Length: 911 amino acids
Theoretical weight: 104.12 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P49917 (Residues: 1-911; Coverage: 100%)
Gene name: LIG4
Sequence domains:
DNA (25-MER) Chain: j
Molecule details ›
Chain: j
Length: 25 nucleotides
Theoretical weight: 7.75 KDa
DNA (27-MER) Chain: i
Molecule details ›
Chain: i
Length: 27 nucleotides
Theoretical weight: 8.29 KDa
DNA (26-MER) Chain: d
Molecule details ›
Chain: d
Length: 26 nucleotides
Theoretical weight: 8.04 KDa
DNA (28-MER) Chain: e
Molecule details ›
Chain: e
Length: 28 nucleotides
Theoretical weight: 8.6 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.55Å
Relevant EMDB volumes: EMD-16044
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli BL21(DE3)