› 6e94

X-ray diffraction
1.59Å resolution

Crystal Structure of ZBTB38 C-terminal Zinc Fingers 6-9 K1055R in complex with methylated DNA

Released:
DOI: 10.2210/pdb6e94/pdb
PDB entry 6e94 coloured by chain, front view.
PDB entry 6e94 coloured by chain, side view.
PDB entry 6e94 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38.
Hudson NO, Whitby FG, Buck-Koehntop BA
J Biol Chem 293 19835-19843 (2018)
PMID: 30355731

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-119836 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Zinc finger and BTB domain-containing protein 38 Chain: A
Molecule details ›
Chain: A
Length: 119 amino acids
Theoretical weight: 14.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8NAP3 (Residues: 1006-1124; Coverage: 10%)
Gene name: ZBTB38
Sequence domains: Zinc finger, C2H2 type
DNA (5'-D(*GP*TP*CP*TP*GP*(DCM)P*GP*CP*(DCM)P*GP*AP*TP*GP*AP*GP*TP*GP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 18 nucleotides
Theoretical weight: 5.58 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*GP*CP*AP*CP*TP*CP*AP*TP*(DCM)P*GP*GP*(DCM)P*GP*CP*AP*GP*AP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 18 nucleotides
Theoretical weight: 5.51 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
1 modified residue:
Ligand 5CM 4 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: C2221
Unit cell:
a: 70.804Å b: 77.27Å c: 103.756Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.194 0.218
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

Sensitivity of transcription factors to DNA methylation.
Héberlé et al. (2019)
1 more

1 mention without citation

Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38.
Hudson et al. (2018)