› 8ezb

Electron Microscopy
8.9Å resolution

NHEJ Long-range complex with ATP

Released:
DOI: 10.2210/pdb8ezb/pdb
PDB entry 8ezb coloured by chain, front view.
PDB entry 8ezb coloured by chain, side view.
PDB entry 8ezb coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Cryo-EM visualization of DNA-PKcs structural intermediates in NHEJ.
Chen S, Vogt A, Lee L, Naila T, McKeown R, Tomkinson AE, Lees-Miller SP, He Y
OpenAccess logo Sci Adv 9 eadg2838 (2023)
PMID: 37256947
Related structures: EMD-28733

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
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero icosamer (preferred)
PDBe Complex ID:
PDB-CPX-217998 (preferred)
Entry contents:
7 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (9 distinct):
X-ray repair cross-complementing protein 6 Chains: A, J
Molecule details ›
Chains: A, J
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: B, K
Molecule details ›
Chains: B, K
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:
DNA-dependent protein kinase catalytic subunit Chains: C, L
Molecule details ›
Chains: C, L
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:
DNA repair protein XRCC4 Chains: F, G, O, P
Molecule details ›
Chains: F, G, O, P
Length: 336 amino acids
Theoretical weight: 38.34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13426 (Residues: 1-336; Coverage: 100%)
Gene name: XRCC4
Sequence domains:
Non-homologous end-joining factor 1 Chains: H, I
Molecule details ›
Chains: H, I
Length: 299 amino acids
Theoretical weight: 33.37 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9H9Q4 (Residues: 1-299; Coverage: 100%)
Gene names: NHEJ1, XLF
Sequence domains:
Protein PAXX Chains: S, T
Molecule details ›
Chains: S, T
Length: 204 amino acids
Theoretical weight: 21.66 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
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 ligase 4 Chains: X, Y
Molecule details ›
Chains: X, Y
Length: 911 amino acids
Theoretical weight: 104.12 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P49917 (Residues: 1-911; Coverage: 100%)
Gene name: LIG4
Sequence domains:
DNA (31-MER) Chains: D, M
Molecule details ›
Chains: D, M
Length: 31 nucleotides
Theoretical weight: 9.51 KDa
DNA (30-MER) Chains: E, N
Molecule details ›
Chains: E, N
Length: 30 nucleotides
Theoretical weight: 9.24 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand ATP 2 x ATP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 8.9Å
Relevant EMDB volumes: EMD-28733
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli

Quick links

Citations

4 review citations

Structure and function of the apical PIKKs in double-strand break repair.
Xu et al. (2023)
3 more