› 3vyq

X-ray diffraction
2.52Å resolution

Crystal structure of the methyl CpG Binding Domain of MBD4 in complex with the 5mCG/TG sequence in space group P1

Released:
DOI: 10.2210/pdb3vyq/pdb
PDB entry 3vyq coloured by chain, front view.
PDB entry 3vyq coloured by chain, side view.
PDB entry 3vyq coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4.
Otani J, Arita K, Kato T, Kinoshita M, Kimura H, Suetake I, Tajima S, Ariyoshi M, Shirakawa M
J Biol Chem 288 6351-62 (2013)
PMID: 23316048

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117067 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Methyl-CpG-binding domain protein 4 Chains: A, D
Molecule details ›
Chains: A, D
Length: 74 amino acids
Theoretical weight: 8.33 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Z2D7 (Residues: 63-136; Coverage: 13%)
Gene name: Mbd4
Sequence domains: Methyl-CpG binding domain
Structure domains: Methyl-cpg-binding Protein 2; Chain A
DNA (5'-D(*AP*CP*AP*TP*CP*(5CM)P*GP*GP*TP*GP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.37 KDa
Source organism: Mus musculus
Expression system: Not provided
DNA (5'-D(*TP*CP*AP*CP*TP*GP*GP*AP*TP*GP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 11 nucleotides
Theoretical weight: 3.36 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 3 x ZN
Ligand EDO 1 x EDO
1 modified residue:
Ligand 5CM 1 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P1
Unit cell:
a: 30.604Å b: 34.093Å c: 61.165Å
α: 75.28° β: 77.76° γ: 87.31°
R-values:
R R work R free
0.195 0.193 0.236
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

18 review citations

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription.
Pastor et al. (2013)
17 more

4 mentions without citation

Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4.
Otani et al. (2013)
3 more