› 7zyg

Electron Microscopy
2.68Å resolution

CryoEM structure of Ku heterodimer bound to DNA, PAXX and XLF

Released:
DOI: 10.2210/pdb7zyg/pdb
PDB entry 7zyg coloured by chain, front view.
PDB entry 7zyg coloured by chain, side view.
PDB entry 7zyg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
PAXX binding to the NHEJ machinery explains functional redundancy with XLF.
Seif-El-Dahan M, Kefala-Stavridi A, Frit P, Hardwick SW, Chirgadze DY, Maia De Oliviera T, Britton S, Barboule N, Bossaert M, Pandurangan AP, Meek K, Blundell TL, Ropars V, Calsou P, Charbonnier JB, Chaplin AK
OpenAccess logo Sci Adv 9 eadg2834 (2023)
PMID: 37256950
Related structures: EMD-15022

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-217215 (preferred)
Entry contents:
4 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (6 distinct):
X-ray repair cross-complementing protein 6 Chain: A
Molecule details ›
Chain: A
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 Chain: B
Molecule details ›
Chain: B
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 Chain: C
Molecule details ›
Chain: C
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
Non-homologous end-joining factor 1 Chain: F
Molecule details ›
Chain: F
Length: 299 amino acids
Theoretical weight: 33.37 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9H9Q4 (Residues: 1-299; Coverage: 100%)
Gene names: NHEJ1, XLF
Sequence domains:
DNA Chain: D
Molecule details ›
Chain: D
Length: 15 nucleotides
Theoretical weight: 4.5 KDa
DNA Chain: E
Molecule details ›
Chain: E
Length: 15 nucleotides
Theoretical weight: 4.67 KDa

Ligands and Environments

1 bound ligand:
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.68Å
Relevant EMDB volumes: EMD-15022
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Holding it together: DNA end synapsis during non-homologous end joining.
Loparo JJ. (2023)
3 other articles