› 4f6n

X-ray diffraction
2.8Å resolution

Crystal structure of Kaiso zinc finger DNA binding protein in complex with methylated CpG site DNA

Released:
DOI: 10.2210/pdb4f6n/pdb
PDB entry 4f6n coloured by chain, front view.
PDB entry 4f6n coloured by chain, side view.
PDB entry 4f6n coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso.
Buck-Koehntop BA, Stanfield RL, Ekiert DC, Martinez-Yamout MA, Dyson HJ, Wilson IA, Wright PE
Proc Natl Acad Sci U S A 109 15229-34 (2012)
PMID: 22949637

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-117466 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Transcriptional regulator Kaiso Chain: A
Molecule details ›
Chain: A
Length: 133 amino acids
Theoretical weight: 16.09 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q86T24 (Residues: 472-604; Coverage: 20%)
Gene names: KAISO, ZBTB33, ZNF348
Structure domains: Classic Zinc Finger
DNA (5'-D(*GP*TP*GP*TP*CP*AP*CP*(5CM)P*GP*(5CM)P*GP*TP*CP*TP*AP*TP*AP*CP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 19 nucleotides
Theoretical weight: 5.82 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*CP*GP*TP*AP*TP*AP*GP*AP*(5CM)P*GP*(5CM)P*GP*GP*TP*GP*AP*CP*AP*C)-3') Chain: E
Molecule details ›
Chain: E
Length: 19 nucleotides
Theoretical weight: 5.88 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 3 x ZN
Ligand GOL 2 x GOL
1 modified residue:
Ligand 5CM 4 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: F222
Unit cell:
a: 44.049Å b: 183.402Å c: 230.138Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.228 0.261
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

17 review citations

Interpreting the language of histone and DNA modifications.
Rothbart et al. (2014)
16 more

10 mentions without citation

On how mammalian transcription factors recognize methylated DNA.
Buck-Koehntop et al. (2013)
9 more