› 5zrf

X-ray diffraction
2.3Å resolution

Crystal structure of human topoisomerase II beta in complex with 5-iodouridine-containing-DNA and etoposide in space group p21

Released:
DOI: 10.2210/pdb5zrf/pdb
PDB entry 5zrf coloured by chain, front view.
PDB entry 5zrf coloured by chain, side view.
PDB entry 5zrf coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate.
Chen SF, Huang NL, Lin JH, Wu CC, Wang YR, Yu YJ, Gilson MK, Chan NL
Nat Commun 9 3085 (2018)
PMID: 30082834

Function and Biology Details

Reaction catalysed: 
ATP-dependent breakage, passage and rejoining of double-stranded DNA
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113206 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct DNA/RNA hybrid molecule
Macromolecules (3 distinct):
DNA topoisomerase 2-beta Chains: A, B
Molecule details ›
Chains: A, B
Length: 803 amino acids
Theoretical weight: 91.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q02880 (Residues: 450-1206; Coverage: 47%)
Gene name: TOP2B
Sequence domains:
DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 8 nucleotides
Theoretical weight: 2.44 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA/RNA (5'-R(P*(IU))-D(P*GP*CP*AP*GP*C)-R(P*(IU))-D(P*CP*GP*GP*C)-R(P*(IU))-3') Chains: D, F
Molecule details ›
Chains: D, F
Length: 12 nucleotides
Theoretical weight: 4.04 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 6 x MG
Ligand EVP 2 x EVP
1 modified residue:
Ligand IU 6 x IU

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL15A1
Spacegroup: P21
Unit cell:
a: 80.147Å b: 176.27Å c: 94.331Å
α: 90° β: 111.44° γ: 90°
R-values:
R R work R free
0.189 0.189 0.226
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

8 review citations

DNA Topoisomerase Inhibitors: Trapping a DNA-Cleaving Machine in Motion.
Bax et al. (2019)
7 more

1 mention without citation

Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate.
Chen et al. (2018)