› 5vmx

X-ray diffraction
2.05Å resolution

Kaiso (ZBTB33) zinc finger DNA binding domain in complex with a hemi CpG-methylated DNA resembling the specific Kaiso binding sequence (KBS)

Released:
DOI: 10.2210/pdb5vmx/pdb
PDB entry 5vmx coloured by chain, front view.
PDB entry 5vmx coloured by chain, side view.
PDB entry 5vmx coloured by chain, top view.
Source organisms:
Primary publication:
CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso.
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE
Biochemistry 57 2109-2120 (2018)
PMID: 29546986

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-119283 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Transcriptional regulator Kaiso Chain: A
Molecule details ›
Chain: A
Length: 134 amino acids
Theoretical weight: 16.22 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q86T24 (Residues: 471-604; Coverage: 20%)
Gene names: KAISO, ZBTB33, ZNF348
DNA (5'-D(*TP*GP*CP*TP*TP*CP*CP*(5CM)P*GP*(5CM)P*GP*AP*AP*TP*AP*AP*CP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 18 nucleotides
Theoretical weight: 5.5 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*CP*GP*CP*GP*GP*GP*AP*AP*GP*CP*A)-3') Chain: E
Molecule details ›
Chain: E
Length: 18 nucleotides
Theoretical weight: 5.56 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: C222
Unit cell:
a: 44.338Å b: 183.984Å c: 105.072Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.165 0.162 0.188
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

Zinc Finger Readers of Methylated DNA.
Hudson et al. (2018)
1 more

1 mention without citation

CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso.
Nikolova et al. (2018)