› 4m9e

X-ray diffraction
1.85Å resolution

Structure of Klf4 zinc finger DNA binding domain in complex with methylated DNA

Released:
DOI: 10.2210/pdb4m9e/pdb
PDB entry 4m9e coloured by chain, front view.
PDB entry 4m9e coloured by chain, side view.
PDB entry 4m9e coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Structural basis for Klf4 recognition of methylated DNA.
Liu Y, Olanrewaju YO, Zheng Y, Hashimoto H, Blumenthal RM, Zhang X, Cheng X
Nucleic Acids Res 42 4859-67 (2014)
PMID: 24520114

Function and Biology Details

Biochemical function:
  • not assigned
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-117835 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Krueppel-like factor 4 Chain: A
Molecule details ›
Chain: A
Length: 88 amino acids
Theoretical weight: 10.43 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q60793 (Residues: 396-483; Coverage: 18%)
Gene names: Ezf, Gklf, Klf4, Zie
Sequence domains: Zinc finger, C2H2 type
DNA (5'-D(*GP*AP*GP*GP*(5CM)P*GP*TP*GP*GP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 10 nucleotides
Theoretical weight: 3.14 KDa
Source organism: Mus musculus
Expression system: Not provided
DNA (5'-D(*GP*CP*CP*AP*(5CM)P*GP*CP*CP*TP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 2.98 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand GOL 1 x GOL
Ligand ACT 1 x ACT
Ligand ZN 3 x ZN
1 modified residue:
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P43212
Unit cell:
a: 48.705Å b: 48.705Å c: 131.015Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.187 0.234
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

10 review citations

Transcription factors as readers and effectors of DNA methylation.
Zhu et al. (2016)
9 more

13 mentions without citation

Evolving insights on how cytosine methylation affects protein-DNA binding.
Dantas Machado et al. (2015)
12 more