› 3vxv

X-ray diffraction
2Å resolution

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

Released:
DOI: 10.2210/pdb3vxv/pdb
PDB entry 3vxv coloured by chain, front view.
PDB entry 3vxv coloured by chain, side view.
PDB entry 3vxv 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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117064 (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: 69 amino acids
Theoretical weight: 7.83 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Z2D7 (Residues: 69-136; Coverage: 12%)
Gene name: Mbd4
Sequence domains: Methyl-CpG binding domain
Structure domains: Methyl-cpg-binding Protein 2; Chain A
DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*CP*(5CM)P*GP*GP*AP*CP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 14 nucleotides
Theoretical weight: 4.26 KDa
Source organism: Mus musculus
Expression system: Not provided
DNA (5'-D(*GP*TP*CP*TP*GP*GP*TP*AP*GP*TP*GP*AP*CP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 14 nucleotides
Theoretical weight: 4.33 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ACT 3 x ACT
Ligand EDO 6 x EDO
1 modified residue:
Ligand 5CM 1 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A, PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: C2221
Unit cell:
a: 89.074Å b: 94.989Å c: 54.738Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.188 0.224
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

16 review citations

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

5 mentions without citation

Role of base excision repair in maintaining the genetic and epigenetic integrity of CpG sites.
Bellacosa et al. (2015)
4 more