› 5zyw

X-ray diffraction
2.2Å resolution

The crystal structure of apo-HsMGME1 with Mn2+

Released:
DOI: 10.2210/pdb5zyw/pdb
PDB entry 5zyw coloured by chain, front view.
PDB entry 5zyw coloured by chain, side view.
PDB entry 5zyw coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insights into DNA degradation by human mitochondrial nuclease MGME1.
Yang C, Wu R, Liu H, Chen Y, Gao Y, Chen X, Li Y, Ma J, Li J, Gan J
Nucleic Acids Res 46 11075-11088 (2018)
PMID: 30247721

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189677 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Mitochondrial genome maintenance exonuclease 1 Chain: A
Molecule details ›
Chain: A
Length: 254 amino acids
Theoretical weight: 29.52 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9BQP7 (Residues: 91-344; Coverage: 74%)
Gene names: C20orf72, DDK1, MGME1
Sequence domains: PD-(D/E)XK nuclease superfamily

Ligands and Environments

3 bound ligands:
Ligand MN 3 x MN
Ligand TLA 1 x TLA
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NFPSS BEAMLINE BL19U1
Spacegroup: P43212
Unit cell:
a: 67.997Å b: 67.997Å c: 114.841Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.227 0.226 0.252
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Mitochondrial DNA: cellular genotoxic stress sentinel.
Wu et al. (2021)
3 more

2 mentions without citation

Mitochondrial DNA degradation: A quality control measure for mitochondrial genome maintenance and stress response.
Zhao L. (2019)
1 more