› 6mdx

X-ray diffraction
1.55Å resolution

Mechanism of protease dependent DPC repair

Released:
DOI: 10.2210/pdb6mdx/pdb
PDB entry 6mdx coloured by chain, front view.
PDB entry 6mdx coloured by chain, side view.
PDB entry 6mdx coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural Insight into DNA-Dependent Activation of Human Metalloprotease Spartan.
Li F, Raczynska JE, Chen Z, Yu H
Cell Rep 26 3336-3346.e4 (2019)
PMID: 30893605

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120283 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DNA-dependent metalloprotease SPRTN Chain: A
Molecule details ›
Chain: A
Length: 185 amino acids
Theoretical weight: 22.06 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9H040 (Residues: 28-214; Coverage: 38%)
Gene names: C1orf124, DVC1, SPRTN, UNQ1880/PRO4323
Sequence domains:
DNA (5'-D(P*CP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 2 nucleotides
Theoretical weight: 533 Da
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand EDO 1 x EDO
Ligand PGE 1 x PGE
Ligand ZN 2 x ZN
Ligand FLC 1 x FLC
2 modified residues:
Ligand MSE 4 x MSE
Ligand MLZ 1 x MLZ

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21212
Unit cell:
a: 128.324Å b: 29.507Å c: 50.298Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.161 0.159 0.193
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 review citations

Debulking of topoisomerase DNA-protein crosslinks (TOP-DPC) by the proteasome, non-proteasomal and non-proteolytic pathways.
Sun et al. (2020)
8 more

2 mentions without citation

DNA Structure-Specific Cleavage of DNA-Protein Crosslinks by the SPRTN Protease.
Reinking et al. (2020)
1 more