› 2wbs

X-ray diffraction
1.7Å resolution

Crystal structure of the zinc finger domain of Klf4 bound to its target DNA

Released:
DOI: 10.2210/pdb2wbs/pdb
PDB entry 2wbs coloured by chain, front view.
PDB entry 2wbs coloured by chain, side view.
PDB entry 2wbs coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
The structure of the Klf4 DNA-binding domain links to self-renewal and macrophage differentiation.
Schuetz A, Nana D, Rose C, Zocher G, Milanovic M, Koenigsmann J, Blasig R, Heinemann U, Carstanjen D
Cell Mol Life Sci 68 3121-31 (2011)
PMID: 21290164

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-115905 (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: 89 amino acids
Theoretical weight: 10.56 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q60793 (Residues: 395-483; Coverage: 18%)
Gene names: Ezf, Gklf, Klf4, Zie
Sequence domains: Zinc finger, C2H2 type
Structure domains: Classic Zinc Finger
5'-D(*GP*AP*GP*GP*CP*GP*CP)-3' Chain: F
Molecule details ›
Chain: F
Length: 7 nucleotides
Theoretical weight: 2.16 KDa
Source organism: Mus musculus
Expression system: Not provided
5'-D(*GP*CP*GP*CP*CP*TP*CP)-3' Chain: G
Molecule details ›
Chain: G
Length: 7 nucleotides
Theoretical weight: 2.07 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 3 x ZN
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: P212121
Unit cell:
a: 41Å b: 45.97Å c: 73.91Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.202 0.2 0.232
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

11 review citations

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

13 mentions without citation

Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming.
Soufi et al. (2015)
12 more