› 5vmv

X-ray diffraction
2.31Å resolution

Kaiso (ZBTB33) zinc finger DNA binding domain in complex with its double CpG-methylated DNA consensus binding site

Released:
DOI: 10.2210/pdb5vmv/pdb
PDB entry 5vmv coloured by chain, front view.
PDB entry 5vmv coloured by chain, side view.
PDB entry 5vmv coloured by chain, top view.
Source organism: Homo sapiens
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-119281 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 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*TP*(5CM)P*GP*(5CM)P*GP*AP*GP*AP*AP*GP*CP*A)-3') Chains: D, E
Molecule details ›
Chains: D, E
Length: 18 nucleotides
Theoretical weight: 5.54 KDa
Source organism: Homo sapiens
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 4 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: C222
Unit cell:
a: 44.219Å b: 183.792Å c: 104.566Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.203 0.247
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

2 mentions without citation

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