› 6df8

X-ray diffraction
2.54Å resolution

Kaiso (ZBTB33) zinc finger DNA binding domain in complex with the specific Kaiso binding sequence (KBS), pH 6.5

Released:
DOI: 10.2210/pdb6df8/pdb
PDB entry 6df8 coloured by chain, front view.
PDB entry 6df8 coloured by chain, side view.
PDB entry 6df8 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A Conformational Switch in the Zinc Finger Protein Kaiso Mediates Differential Readout of Specific and Methylated DNA Sequences.
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE
Biochemistry 59 1909-1926 (2020)
PMID: 32352758

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-119732 (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*TP*GP*CP*CP*AP*AP*TP*AP*AP*CP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 18 nucleotides
Theoretical weight: 5.45 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*GP*GP*CP*AP*GP*GP*AP*AP*GP*CP*A)-3') Chain: E
Molecule details ›
Chain: E
Length: 18 nucleotides
Theoretical weight: 5.58 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
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: C222
Unit cell:
a: 44.371Å b: 184.267Å c: 104.938Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.179 0.222
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 review citation

Insights from the protein interaction Universe of the multifunctional "Goldilocks" kinase DYRK1A.
Ananthapadmanabhan et al. (2023)
5 other articles

1 mention without citation

A Conformational Switch in the Zinc Finger Protein Kaiso Mediates Differential Readout of Specific and Methylated DNA Sequences.
Nikolova et al. (2020)