› 6ml7

X-ray diffraction
1.75Å resolution

ZBTB24 Zinc Fingers 4-8 with 19+1mer DNA Oligonucleotide (Sequence 4 with a CpG 5mC Modification)

Released:
DOI: 10.2210/pdb6ml7/pdb
PDB entry 6ml7 coloured by chain, front view.
PDB entry 6ml7 coloured by chain, side view.
PDB entry 6ml7 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Structural basis of specific DNA binding by the transcription factor ZBTB24.
Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK, Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H, Zhang X, Chen T, Cheng X
Nucleic Acids Res 47 8388-8398 (2019)
PMID: 31226215

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-120298 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Zinc finger and BTB domain-containing protein 24 Chain: A
Molecule details ›
Chain: A
Length: 151 amino acids
Theoretical weight: 17.27 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q80X44 (Residues: 375-519; Coverage: 20%)
Gene names: Bif1, Bsg1, Zbtb24, Znf450
Sequence domains: Zinc finger, C2H2 type
DNA (5'-D(*AP*CP*GP*CP*AP*GP*GP*TP*CP*CP*TP*GP*GP*AP*(5CM)P*GP*AP*AP*TP*T)-3') Chain: E
Molecule details ›
Chain: E
Length: 20 nucleotides
Theoretical weight: 6.17 KDa
Source organism: Mus musculus
Expression system: Not provided
DNA (5'-D(*TP*AP*AP*TP*TP*CP*GP*TP*CP*CP*AP*GP*GP*AP*CP*CP*TP*GP*CP*G)-3') Chain: F
Molecule details ›
Chain: F
Length: 20 nucleotides
Theoretical weight: 6.11 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-003
Spacegroup: P21
Unit cell:
a: 46.13Å b: 68.707Å c: 48.448Å
α: 90° β: 92.58° γ: 90°
R-values:
R R work R free
0.195 0.193 0.24
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

5 review citations

Understanding the Relevance of DNA Methylation Changes in Immune Differentiation and Disease.
Calle-Fabregat et al. (2020)
4 more

2 mentions without citation

Identification of a novel dual-target scaffold for 3CLpro and RdRp proteins of SARS-CoV-2 using 3D-similarity search, molecular docking, molecular dynamics and ADMET evaluation.
Aouidate et al. (2021)
1 more