› 4e9f

X-ray diffraction
1.79Å resolution

Structure of the glycosylase domain of MBD4 bound to AP site containing DNA

Released:
DOI: 10.2210/pdb4e9f/pdb
PDB entry 4e9f coloured by chain, front view.
PDB entry 4e9f coloured by chain, side view.
PDB entry 4e9f coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Biochemical and structural characterization of the glycosylase domain of MBD4 bound to thymine and 5-hydroxymethyuracil-containing DNA.
Moréra S, Grin I, Vigouroux A, Couvé S, Henriot V, Saparbaev M, Ishchenko AA
Nucleic Acids Res 40 9917-26 (2012)
PMID: 22848106

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117393 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Methyl-CpG-binding domain protein 4 Chain: A
Molecule details ›
Chain: A
Length: 161 amino acids
Theoretical weight: 19.42 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O95243 (Residues: 427-580; Coverage: 27%)
Gene names: MBD4, MED1
Structure domains: Hypothetical protein; domain 2
DNA (5'-D(*CP*CP*AP*GP*CP*GP*(3DR)P*GP*CP*AP*GP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.52 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P212121
Unit cell:
a: 41.07Å b: 55.84Å c: 96.65Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.214 0.248
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

19 review citations

Base excision repair of oxidative DNA damage: from mechanism to disease.
Whitaker et al. (2017)
18 more

2 mentions without citation

Biochemical and structural characterization of the glycosylase domain of MBD4 bound to thymine and 5-hydroxymethyuracil-containing DNA.
Moréra et al. (2012)
1 more