› 5kl5

X-ray diffraction
2.29Å resolution

Wilms Tumor Protein (WT1) ZnF2-4 Q369H in complex with carboxylated DNA

Released:
DOI: 10.2210/pdb5kl5/pdb
PDB entry 5kl5 coloured by chain, front view.
PDB entry 5kl5 coloured by chain, side view.
PDB entry 5kl5 coloured by chain, top view.
Source organisms:
Primary publication:
Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications.
Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng X
Nucleic Acids Res 44 10165-10176 (2016)
PMID: 27596598

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-118955 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Wilms tumor protein Chain: A
Molecule details ›
Chain: A
Length: 93 amino acids
Theoretical weight: 11.29 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P19544 (Residues: 350-440; Coverage: 20%)
Gene name: WT1
Sequence domains: Zinc finger, C2H2 type
Structure domains: Classic Zinc Finger
DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(1CC)P*GP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.47 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*CP*GP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 11 nucleotides
Theoretical weight: 3.29 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 3 x ZN
Ligand EDO 1 x EDO
2 modified residues:
Ligand 1CC 1 x 1CC
Ligand 5CM 1 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P21212
Unit cell:
a: 67.493Å b: 77.211Å c: 35.794Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.193 0.246
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

Molecular update on biology of Wilms Tumor 1 gene and its applications in acute myeloid leukemia.
Goel et al. (2020)
1 more