› 2moe

Solution NMR

Solution structure of MBD4 methyl-cytosine binding domain bound to methylated DNA

Released:
DOI: 10.2210/pdb2moe/pdb
PDB entry 2moe coloured by chain, ensemble of 20 models, front view.
PDB entry 2moe coloured by chain, ensemble of 20 models, side view.
PDB entry 2moe coloured by chain, ensemble of 20 models, top view.
Source organism: Homo sapiens
Primary publication:
Solution structure and intramolecular exchange of methyl-cytosine binding domain protein 4 (MBD4) on DNA suggests a mechanism to scan for mCpG/TpG mismatches.
Walavalkar NM, Cramer JM, Buchwald WA, Scarsdale JN, Williams DC
Nucleic Acids Res 42 11218-32 (2014)
PMID: 25183517

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-115638 (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: 71 amino acids
Theoretical weight: 8.09 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: O95243 (Residues: 80-148; Coverage: 12%)
Gene names: MBD4, MED1
Sequence domains: Methyl-CpG binding domain
Structure domains: Methyl-cpg-binding Protein 2; Chain A
DNA (5'-D(*GP*GP*AP*TP*(5CM)P*GP*GP*CP*TP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 10 nucleotides
Theoretical weight: 3.08 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*GP*AP*GP*CP*(5CM)P*GP*AP*TP*CP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 3.04 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
Chemical shift assignment: 62%
Refinement method: simulated annealing
Expression system: Not provided

Quick links

Citations

6 review citations

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

6 mentions without citation

Detecting and interpreting DNA methylation marks.
Ren et al. (2018)
5 more