› 5zen

X-ray diffraction
2.75Å resolution

Crystal structure of human topoisomerase II beta in complex with DNA: a new quaternary conformation showing opening of the protein-linked DNA-gate

Released:
DOI: 10.2210/pdb5zen/pdb
PDB entry 5zen coloured by chain, front view.
PDB entry 5zen coloured by chain, side view.
PDB entry 5zen 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-119502 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA topoisomerase 2-beta Chain: A
Molecule details ›
Chain: A
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') Chain: B
Molecule details ›
Chain: B
Length: 8 nucleotides
Theoretical weight: 2.44 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*AP*GP*CP*TP*CP*GP*GP*CP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 9 nucleotides
Theoretical weight: 2.73 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MN 2 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL13C1
Spacegroup: P3221
Unit cell:
a: 95.76Å b: 95.76Å c: 231.055Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.224 0.221 0.266
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

3 mentions without citation

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