› 4gfh

X-ray diffraction
4.41Å resolution

Topoisomerase II-DNA-AMPPNP complex

Released:
DOI: 10.2210/pdb4gfh/pdb
PDB entry 4gfh coloured by chain, front view.
PDB entry 4gfh coloured by chain, side view.
PDB entry 4gfh coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structure of a topoisomerase II-DNA-nucleotide complex reveals a new control mechanism for ATPase activity.
Schmidt BH, Osheroff N, Berger JM
Nat Struct Mol Biol 19 1147-54 (2012)
PMID: 23022727

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 decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117543 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
Macromolecules (5 distinct):
DNA topoisomerase 2 Chains: A, F
Molecule details ›
Chains: A, F
Length: 1177 amino acids
Theoretical weight: 136.36 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Not provided
UniProt:
  • Canonical: P06786 (Residues: 1-1177; Coverage: 82%)
Gene names: N2244, TOP2, TOR3, YNL088W
Sequence domains:
DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3') Chains: B, G
Molecule details ›
Chains: B, G
Length: 11 nucleotides
Theoretical weight: 3.27 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Not provided
DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)-3') Chains: C, H
Molecule details ›
Chains: C, H
Length: 15 nucleotides
Theoretical weight: 4.68 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Not provided
DNA (5'-D(P*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*(TSP))-3') Chains: D, I
Molecule details ›
Chains: D, I
Length: 11 nucleotides
Theoretical weight: 3.43 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Not provided
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)-3') Chains: E, J
Molecule details ›
Chains: E, J
Length: 15 nucleotides
Theoretical weight: 4.53 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand ANP 2 x ANP
2 modified residues:
Ligand PTR 2 x PTR
Ligand TSP 2 x TSP

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: P212121
Unit cell:
a: 169.135Å b: 169.884Å c: 169.212Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.241 0.239 0.275
Expression system: Not provided

Quick links

Citations

13 review citations

Drugging topoisomerases: lessons and challenges.
Pommier Y. (2013)
12 more

31 mentions without citation

DNA topoisomerases: Advances in understanding of cellular roles and multi-protein complexes via structure-function analysis.
McKie et al. (2021)
30 more