› 6cc8

X-ray diffraction
1.95Å resolution

Crystal structure MBD3 MBD domain in complex with methylated CpG DNA

Released:
DOI: 10.2210/pdb6cc8/pdb
PDB entry 6cc8 coloured by chain, front view.
PDB entry 6cc8 coloured by chain, side view.
PDB entry 6cc8 coloured by chain, top view.
Source organisms:
Primary publication:
Structural analyses reveal that MBD3 is a methylated CG binder.
Liu K, Lei M, Wu Z, Gan B, Cheng H, Li Y, Min J
FEBS J 286 3240-3254 (2019)
PMID: 30980593

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-119657 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Methyl-CpG-binding domain protein 3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 73 amino acids
Theoretical weight: 8.47 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O95983 (Residues: 1-71; Coverage: 24%)
Gene name: MBD3
Sequence domains: Methyl-CpG binding domain
Structure domains: Methyl-cpg-binding Protein 2; Chain A
methylated CpG DNA 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 12 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: C2
Unit cell:
a: 71.55Å b: 36.64Å c: 130.93Å
α: 90° β: 92.77° γ: 90°
R-values:
R R work R free
0.226 0.224 0.259
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

1 review citation

The Methyl-CpG-Binding Domain 2 and 3 Proteins and Formation of the Nucleosome Remodeling and Deacetylase Complex.
Leighton et al. (2020)
6 other articles

1 mention without citation

Crystal structure of the EcoKMcrA N-terminal domain (NEco): recognition of modified cytosine bases without flipping.
Slyvka et al. (2019)