› 6cnq

X-ray diffraction
2.15Å resolution

MBD2 in complex with methylated DNA

Released:
DOI: 10.2210/pdb6cnq/pdb
PDB entry 6cnq coloured by chain, front view.
PDB entry 6cnq coloured by chain, side view.
PDB entry 6cnq 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-119675 (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: 79 amino acids
Theoretical weight: 8.79 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*AP*(5CM)P*GP*TP*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

1 bound ligand:
Ligand UNX 4 x UNX
1 modified residue:
Ligand 5CM 4 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P31
Unit cell:
a: 40.5Å b: 40.5Å c: 202.896Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.206 0.206 0.229
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

5 mentions without citation

Rational targeting of a NuRD subcomplex guided by comprehensive in situ mutagenesis.
Sher et al. (2019)
4 more