› 5zyv

X-ray diffraction
2.72Å resolution

Crystal structure of human MGME1 with single strand DNA2 and Ca2+

Released:
DOI: 10.2210/pdb5zyv/pdb
PDB entry 5zyv coloured by chain, front view.
PDB entry 5zyv coloured by chain, side view.
PDB entry 5zyv coloured by chain, top view.
Source organisms:
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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119539 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Mitochondrial genome maintenance exonuclease 1 Chain: A
Molecule details ›
Chain: A
Length: 254 amino acids
Theoretical weight: 29.51 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
DNA (5'-D(P*CP*AP*AP*CP*AP*AP*T)-3') Chain: E
Molecule details ›
Chain: E
Length: 15 nucleotides
Theoretical weight: 4.53 KDa
Source organism: unidentified
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CA 2 x CA
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P21212
Unit cell:
a: 81.282Å b: 106.151Å c: 33.391Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.212 0.254
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

5 review citations

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

3 mentions without citation

Structural insights into DNA degradation by human mitochondrial nuclease MGME1.
Yang et al. (2018)
2 more