› 4r2s

X-ray diffraction
2.49Å resolution

Wilms Tumor Protein (WT1) Q369P zinc fingers in complex with methylated DNA

Released:
DOI: 10.2210/pdb4r2s/pdb
PDB entry 4r2s coloured by chain, front view.
PDB entry 4r2s coloured by chain, side view.
PDB entry 4r2s coloured by chain, top view.
Source organisms:
Primary publication:
Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence.
Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang X, Cheng X
Genes Dev 28 2304-13 (2014)
PMID: 25258363

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-118063 (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: 11.25 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*(5CM)P*GP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.44 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 2 x EDO
1 modified residue:
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: C2
Unit cell:
a: 69.148Å b: 66.575Å c: 36.073Å
α: 90° β: 93.32° γ: 90°
R-values:
R R work R free
0.21 0.208 0.268
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

29 review citations

TET-mediated active DNA demethylation: mechanism, function and beyond.
Wu et al. (2017)
28 more

5 mentions without citation

Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence.
Hashimoto et al. (2014)
4 more