› 6erf

X-ray diffraction
3.01Å resolution

Complex of APLF factor and Ku heterodimer bound to DNA

Released:
DOI: 10.2210/pdb6erf/pdb
PDB entry 6erf coloured by chain, front view.
PDB entry 6erf coloured by chain, side view.
PDB entry 6erf coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining.
Nemoz C, Ropars V, Frit P, Gontier A, Drevet P, Yu J, Guerois R, Pitois A, Comte A, Delteil C, Barboule N, Legrand P, Baconnais S, Yin Y, Tadi S, Barbet-Massin E, Berger I, Le Cam E, Modesti M, Rothenberg E, Calsou P, Charbonnier JB
Nat Struct Mol Biol 25 971-980 (2018)
PMID: 30291363

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119853 (preferred)
Entry contents:
3 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (5 distinct):
X-ray repair cross-complementing protein 6 Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 544 amino acids
Theoretical weight: 62.63 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P12956 (Residues: 1-544; Coverage: 89%)
Gene names: G22P1, XRCC6
Sequence domains:
Structure domains:
X-ray repair cross-complementing protein 5 Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 572 amino acids
Theoretical weight: 65.36 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P13010 (Residues: 2-555; Coverage: 76%)
Gene names: G22P2, XRCC5
Sequence domains:
Structure domains:
Aprataxin and PNK-like factor Chains: Q, R, S, T
Molecule details ›
Chains: Q, R, S, T
Length: 18 amino acids
Theoretical weight: 2.23 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q8IW19 (Residues: 174-191; Coverage: 4%)
Gene names: APLF, C2orf13, PALF, XIP1
DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3') Chains: I, K, M, O
Molecule details ›
Chains: I, K, M, O
Length: 21 nucleotides
Theoretical weight: 6.51 KDa
DNA (34-MER) Chains: J, L, N, P
Molecule details ›
Chains: J, L, N, P
Length: 34 nucleotides
Theoretical weight: 10.33 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P1
Unit cell:
a: 98.92Å b: 140.86Å c: 150.31Å
α: 68.64° β: 80.85° γ: 81.23°
R-values:
R R work R free
0.21 0.209 0.227
Expression systems:
  • Spodoptera frugiperda
  • Not provided

Quick links

Citations

14 review citations

The molecular basis and disease relevance of non-homologous DNA end joining.
Zhao et al. (2020)
13 more

7 mentions without citation

SPOC domain proteins in health and disease.
Appel et al. (2023)
6 more