› 6mdw

X-ray diffraction
1.5Å resolution

Mechanism of protease dependent DPC repair

Released:
DOI: 10.2210/pdb6mdw/pdb
PDB entry 6mdw coloured by chain, front view.
PDB entry 6mdw coloured by chain, side view.
PDB entry 6mdw 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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190467 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA-dependent metalloprotease SPRTN Chain: A
Molecule details ›
Chain: A
Length: 194 amino acids
Theoretical weight: 22.71 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9H040 (Residues: 26-214; Coverage: 39%)
Gene names: C1orf124, DVC1, SPRTN, UNQ1880/PRO4323
Sequence domains: SprT-like family

Ligands and Environments

4 bound ligands:
Ligand FLC 1 x FLC
Ligand ADP 1 x ADP
Ligand EDO 1 x EDO
Ligand ZN 2 x ZN
1 modified residue:
Ligand MLZ 1 x MLZ

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21212
Unit cell:
a: 128.422Å b: 29.553Å c: 50.242Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.165 0.163 0.193
Expression system: Escherichia coli

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

4 mentions without citation

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