› 4ew4

X-ray diffraction
2.79Å resolution

mouse MBD4 glycosylase domain in complex with DNA containing a ribose sugar

Released:
DOI: 10.2210/pdb4ew4/pdb
PDB entry 4ew4 coloured by chain, front view.
PDB entry 4ew4 coloured by chain, side view.
PDB entry 4ew4 coloured by chain, top view.
Source organisms:
Primary publication:
Excision of thymine and 5-hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylation.
Hashimoto H, Zhang X, Cheng X
Nucleic Acids Res 40 8276-84 (2012)
PMID: 22740654

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-117437 (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: 146 amino acids
Theoretical weight: 17.56 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Z2D7 (Residues: 411-554; Coverage: 26%)
Gene name: Mbd4
Structure domains: Hypothetical protein; domain 2
DNA (5'-D(*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.37 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*CP*AP*TP*GP*(3DR)P*GP*CP*TP*GP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 11 nucleotides
Theoretical weight: 3.23 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand NI 1 x NI
Ligand UNX 1 x UNX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: C2221
Unit cell:
a: 40.12Å b: 110.3Å c: 119.71Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.26 0.259 0.277
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

15 review citations

Base excision repair.
Krokan et al. (2013)
14 more

4 mentions without citation

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