› 7nfe

Electron Microscopy
4.29Å resolution

Cryo-EM structure of NHEJ super-complex (monomer)

Released:
DOI: 10.2210/pdb7nfe/pdb
PDB entry 7nfe coloured by chain, front view.
PDB entry 7nfe coloured by chain, side view.
PDB entry 7nfe coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Cryo-EM of NHEJ supercomplexes provides insights into DNA repair.
Chaplin AK, Hardwick SW, Stavridi AK, Buehl CJ, Goff NJ, Ropars V, Liang S, De Oliveira TM, Chirgadze DY, Meek K, Charbonnier JB, Blundell TL
OpenAccess logo Mol Cell 81 3400-3409.e3 (2021)
PMID: 34352203
Related structures: EMD-12301

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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-121693 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (8 distinct):
DNA-dependent protein kinase catalytic subunit Chain: A
Molecule details ›
Chain: A
Length: 4156 amino acids
Theoretical weight: 472.06 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 Chain: B
Molecule details ›
Chain: B
Length: 609 amino acids
Theoretical weight: 69.95 KDa
Source organism: Homo sapiens
Expression system: Insect cell expression vector pTIE1
UniProt:
  • Canonical: P12956 (Residues: 1-609; Coverage: 100%)
Gene names: G22P1, XRCC6
Sequence domains:
X-ray repair cross-complementing protein 5 Chain: C
Molecule details ›
Chain: C
Length: 732 amino acids
Theoretical weight: 82.81 KDa
Source organism: Homo sapiens
Expression system: Insect cell expression vector pTIE1
UniProt:
  • Canonical: P13010 (Residues: 1-732; Coverage: 100%)
Gene names: G22P2, XRCC5
Sequence domains:
Non-homologous end-joining factor 1 Chains: F, G
Molecule details ›
Chains: F, G
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 repair protein XRCC4 Chains: H, I
Molecule details ›
Chains: H, I
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 Chain: J
Molecule details ›
Chain: J
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 (5'-D(P*AP*AP*TP*AP*AP*AP*CP*TP*AP*AP*AP*AP*AP*CP*TP*AP*TP*TP*AP*TP*TP*AP*TP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 24 nucleotides
Theoretical weight: 7.37 KDa
DNA (5'-D(P*TP*AP*AP*TP*AP*AP*TP*AP*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*AP*G)-3') Chain: E
Molecule details ›
Chain: E
Length: 24 nucleotides
Theoretical weight: 7.4 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.29Å
Relevant EMDB volumes: EMD-12301
Expression systems:
  • Insect cell expression vector pTIE1
  • Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

Function and Molecular Mechanism of the DNA Damage Response in Immunity and Cancer Immunotherapy.
Ye et al. (2021)
9 more

3 mentions without citation

Cryo-EM of NHEJ supercomplexes provides insights into DNA repair.
Chaplin et al. (2021)
2 more