› 5keb

X-ray diffraction
2.45Å resolution

mouse Klf4 ZnF1-3 (E446D) and CpG/CpG sequence DNA complex structure: Form II

Released:
DOI: 10.2210/pdb5keb/pdb
PDB entry 5keb coloured by chain, front view.
PDB entry 5keb coloured by chain, side view.
PDB entry 5keb coloured by chain, top view.
Source organisms:
Primary publication:
Distinctive Klf4 mutants determine preference for DNA methylation status.
Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM, Zhang X, Cheng X
Nucleic Acids Res 44 10177-10185 (2016)
PMID: 27596594

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-118908 (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: 93 amino acids
Theoretical weight: 10.83 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
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*CP*GP*TP*GP*GP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 10 nucleotides
Theoretical weight: 3.13 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*CP*CP*AP*CP*GP*CP*CP*TP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 2.97 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P43212
Unit cell:
a: 51.11Å b: 51.11Å c: 131.58Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.25 0.248 0.286
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

DNA Methylation Readers and Cancer: Mechanistic and Therapeutic Applications.
Mahmood et al. (2019)
2 more

1 mention without citation

On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF.
Meseguer et al. (2020)