› 5tvp

X-ray diffraction
2.4Å resolution

SUMO2 bound to Mouse Tdp2 catalytic domain with a 5'-phosphorylated DNA ternary complex

Released:
DOI: 10.2210/pdb5tvp/pdb
Model geometry
Fit model/data
PDB entry 5tvp coloured by chain, front view.
PDB entry 5tvp coloured by chain, side view.
PDB entry 5tvp coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
ZATT (ZNF451)-mediated resolution of topoisomerase 2 DNA-protein cross-links.
Schellenberg MJ, Lieberman JA, Herrero-Ruiz A, Butler LR, Williams JG, Muñoz-Cabello AM, Mueller GA, London RE, Cortés-Ledesma F, Williams RS
Science 357 1412-1416 (2017)
PMID: 28912134

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero tetramer
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-218994 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (3 distinct):
Tyrosyl-DNA phosphodiesterase 2 Chains: A, B, E, G, I, K, M, O
Molecule details ›
Chains: A, B, E, G, I, K, M, O
Length: 256 amino acids
Theoretical weight: 28.91 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9JJX7 (Residues: 118-370; Coverage: 68%)
Gene names: Tdp2, Ttrap
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase
Small ubiquitin-related modifier 2 Chain: Q
Molecule details ›
Chain: Q
Length: 81 amino acids
Theoretical weight: 9.37 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P61957 (Residues: 10-88; Coverage: 83%)
Gene names: Smt3b, Smt3h2, Sumo2
Sequence domains: Ubiquitin-2 like Rad60 SUMO-like
DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3') Chains: C, D, F, H, J, L, N, P

Ligands and Environments

3 bound ligands:
Ligand PO4 9 x PO4
Ligand EDO 13 x EDO
Ligand CL 3 x CL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 106.547Å b: 113.772Å c: 125.434Å
α: 90° β: 91.52° γ: 90°
R-values:
R R work R free
0.193 0.191 0.233
Expression system: Escherichia coli

Quick links

Citations

29 review citations

Replication-Coupled DNA Repair.
Cortez D. (2019)
28 more

1 mention without citation

ZATT (ZNF451)-mediated resolution of topoisomerase 2 DNA-protein cross-links.
Schellenberg et al. (2017)