› 6vjw

X-ray diffraction
2.02Å resolution

Crystal structure of WT hMBD4 complexed with T:G mismatch DNA

Released:
DOI: 10.2210/pdb6vjw/pdb
PDB entry 6vjw coloured by chain, front view.
PDB entry 6vjw coloured by chain, side view.
PDB entry 6vjw coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Catalytic mechanism of the mismatch-specific DNA glycosylase methyl-CpG-binding domain 4.
Ouzon-Shubeita H, Jung H, Lee MH, Koag MC, Lee S
Biochem J 477 1601-1612 (2020)
PMID: 32297632

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-511162 (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: 138 amino acids
Theoretical weight: 16.61 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O95243 (Residues: 438-575; Coverage: 24%)
Gene names: MBD4, MED1
DNA (5'-D(*CP*CP*AP*GP*CP*GP*(ORP)P*GP*CP*AP*GP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.54 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: P212121
Unit cell:
a: 40.35Å b: 58.433Å c: 101.142Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.219 0.219 0.263
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 citations in other articles

Insights into the substrate discrimination mechanisms of methyl-CpG-binding domain 4.
Ouzon-Shubeita et al. (2021)

2 mentions without citation

Structural Insights into the Mechanism of Base Excision by MBD4.
Pidugu et al. (2021)
1 more