› 6b0o

X-ray diffraction
1.55Å resolution

Zinc finger Domain of WT1(-KTS form) with 12+1mer Oligonucleotide with 3' Triplet TGT

Released:
DOI: 10.2210/pdb6b0o/pdb
PDB entry 6b0o coloured by chain, front view.
PDB entry 6b0o coloured by chain, side view.
PDB entry 6b0o coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Role for first zinc finger of WT1 in DNA sequence specificity: Denys-Drash syndrome-associated WT1 mutant in ZF1 enhances affinity for a subset of WT1 binding sites.
Wang D, Horton JR, Zheng Y, Blumenthal RM, Zhang X, Cheng X
Nucleic Acids Res 46 3864-3877 (2018)
PMID: 29294058

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-119590 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Wilms tumor protein Chains: A, D
Molecule details ›
Chains: A, D
Length: 119 amino acids
Theoretical weight: 14.63 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P19544 (Residues: 321-440; Coverage: 26%)
Gene name: WT1
Sequence domains: Zinc finger, C2H2 type
DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*GP*TP*GP*T)-3') Chains: B, E
Molecule details ›
Chains: B, E
Length: 13 nucleotides
Theoretical weight: 4.09 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*TP*AP*CP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 13 nucleotides
Theoretical weight: 3.86 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P1
Unit cell:
a: 36.927Å b: 42.657Å c: 71.821Å
α: 88.28° β: 77.71° γ: 85.81°
R-values:
R R work R free
0.193 0.193 0.206
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Not provided

Quick links

Citations

2 review citations

Disorder and cysteines in proteins: A design for orchestration of conformational see-saw and modulatory functions.
Bhopatkar et al. (2020)
1 more

2 mentions without citation

Role for first zinc finger of WT1 in DNA sequence specificity: Denys-Drash syndrome-associated WT1 mutant in ZF1 enhances affinity for a subset of WT1 binding sites.
Wang et al. (2018)
1 more