› 6cnp

X-ray diffraction
2.1Å resolution

Crystal structure of MBD2 complex with methylated CpG island

Released:
DOI: 10.2210/pdb6cnp/pdb
PDB entry 6cnp coloured by chain, front view.
PDB entry 6cnp coloured by chain, side view.
PDB entry 6cnp coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA.
Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min J
J Biol Chem 293 7344-7354 (2018)
PMID: 29567833

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-119674 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Methyl-CpG-binding domain protein 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 96 amino acids
Theoretical weight: 10.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UBB5 (Residues: 143-220; Coverage: 19%)
Gene name: MBD2
Sequence domains: Methyl-CpG binding domain
Structure domains: Methyl-cpg-binding Protein 2; Chain A
DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3') Chains: C, D, E, F
Molecule details ›
Chains: C, D, E, F
Length: 12 nucleotides
Theoretical weight: 3.68 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CA 1 x CA
Ligand UNX 11 x UNX
1 modified residue:
Ligand 5CM 4 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P1
Unit cell:
a: 40.96Å b: 41.32Å c: 58.67Å
α: 101.57° β: 99.46° γ: 100.54°
R-values:
R R work R free
0.191 0.189 0.218
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

7 review citations

Toward a Mechanistic Understanding of DNA Methylation Readout by Transcription Factors.
Kribelbauer et al. (2020)
6 more

3 mentions without citation

Protein Interactions at Oxidized 5-Methylcytosine Bases.
Pfeifer et al. (2020)
2 more