› 4dk9

X-ray diffraction
2.76Å resolution

Crystal Structure of MBD4 Catalytic Domain Bound to Abasic DNA

Released:
DOI: 10.2210/pdb4dk9/pdb
PDB entry 4dk9 coloured by chain, front view.
PDB entry 4dk9 coloured by chain, side view.
PDB entry 4dk9 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of human methyl-binding domain IV glycosylase bound to abasic DNA.
Manvilla BA, Maiti A, Begley MC, Toth EA, Drohat AC
J Mol Biol 420 164-75 (2012)
PMID: 22560993

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117320 (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: 157 amino acids
Theoretical weight: 18.67 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O95243 (Residues: 426-580; Coverage: 27%)
Gene names: MBD4, MED1
Structure domains: Hypothetical protein; domain 2
5'-D(*AP*AP*GP*AP*CP*GP*TP*GP*GP*AP*C)-3' Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.41 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3' Chain: C
Molecule details ›
Chain: C
Length: 11 nucleotides
Theoretical weight: 3.19 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand K 1 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P212121
Unit cell:
a: 40.999Å b: 55.161Å c: 122.193Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.234 0.234 0.259
Expression systems:
  • Escherichia coli
  • 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

Recent advances in the structural mechanisms of DNA glycosylases.
Brooks et al. (2013)
5 more