› 5t9j

X-ray diffraction
3Å resolution

Crystal Structure of human GEN1 in complex with Holliday junction DNA in the upper interface

Released:
DOI: 10.2210/pdb5t9j/pdb
PDB entry 5t9j coloured by chain, front view.
PDB entry 5t9j coloured by chain, side view.
PDB entry 5t9j coloured by chain, top view.
Source organisms:
Primary publication:
Human Holliday junction resolvase GEN1 uses a chromodomain for efficient DNA recognition and cleavage.
Lee SH, Princz LN, Klügel MF, Habermann B, Pfander B, Biertümpfel C
Elife 4 (2015)
PMID: 26682650

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero pentamer (preferred)
hetero hexamer
Assembly name:
PDBe Complex ID:
PDB-CPX-119144 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
Macromolecules (5 distinct):
Flap endonuclease GEN homolog 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 506 amino acids
Theoretical weight: 58.39 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q17RS7 (Residues: 1-505; Coverage: 56%)
Gene name: GEN1
Sequence domains:
DNA (5'-D(*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DAP*DGP*DGP*DGP*DAP*DTP*DGP*DC)-3') Chain: C
Molecule details ›
Chain: C
Length: 20 nucleotides
Theoretical weight: 6.13 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*DGP*DCP*DAP*DTP*DCP*DCP*DCP*DTP*DAP*DAP*DGP*DCP*DTP*DCP*DCP*DAP*DTP*DCP*DGP*DT)-3') Chain: D
Molecule details ›
Chain: D
Length: 20 nucleotides
Theoretical weight: 6.16 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*DAP*DCP*DGP*DAP*DTP*DGP*DGP*DAP*DGP*DCP*DCP*DGP*DCP*DTP*DAP*DGP*DGP*DCP*DTP*DC)-3') Chain: E
Molecule details ›
Chain: E
Length: 20 nucleotides
Theoretical weight: 6.03 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*DGP*DAP*DGP*DCP*DCP*DTP*DAP*DGP*DCP*DGP*DTP*DCP*DCP*DGP*DGP*DAP*DAP*DTP*DTP*DC)-3') Chain: F
Molecule details ›
Chain: F
Length: 20 nucleotides
Theoretical weight: 6.21 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand GOL 15 x GOL
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P32
Unit cell:
a: 86.94Å b: 86.94Å c: 200.724Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.201 0.199 0.241
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

4 review citations

DNA Holliday Junction: History, Regulation and Bioactivity.
Song et al. (2022)
3 more

6 mentions without citation

Structural Aspects of DNA Repair and Recombination in Crop Improvement.
Verma et al. (2020)
5 more