5KL5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report



Literature

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, G.G.Cheng, X.

(2016) Nucleic Acids Res 44: 10165-10176

  • DOI: 10.1093/nar/gkw766
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Mutations in human zinc-finger transcription factor WT1 result in abnormal development of the kidneys and genitalia and an array of pediatric problems including nephropathy, blastoma, gonadal dysgenesis and genital discordance. Several overlapping ph ...

    Mutations in human zinc-finger transcription factor WT1 result in abnormal development of the kidneys and genitalia and an array of pediatric problems including nephropathy, blastoma, gonadal dysgenesis and genital discordance. Several overlapping phenotypes are associated with WT1 mutations, including Wilms tumors, Denys-Drash syndrome (DDS), Frasier syndrome (FS) and WAGR syndrome (Wilms tumor, aniridia, genitourinary malformations, and mental retardation). These conditions vary in severity from individual to individual; they can be fatal in early childhood, or relatively benign into adulthood. DDS mutations cluster predominantly in zinc fingers (ZF) 2 and 3 at the C-terminus of WT1, which together with ZF4 determine the sequence-specificity of DNA binding. We examined three DDS associated mutations in ZF2 of human WT1 where the normal glutamine at position 369 is replaced by arginine (Q369R), lysine (Q369K) or histidine (Q369H). These mutations alter the sequence-specificity of ZF2, we find, changing its affinity for certain bases and certain epigenetic forms of cytosine. X-ray crystallography of the DNA binding domains of normal WT1, Q369R and Q369H in complex with preferred sequences revealed the molecular interactions responsible for these affinity changes. DDS is inherited in an autosomal dominant fashion, implying a gain of function by mutant WT1 proteins. This gain, we speculate, might derive from the ability of the mutant proteins to sequester WT1 into unproductive oligomers, or to erroneously bind to variant target sequences.


    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA xcheng@emory.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Wilms tumor proteinA93Homo sapiensMutation(s): 1 
Gene Names: WT1
Find proteins for P19544 (Homo sapiens)
Explore P19544 
Go to UniProtKB:  P19544
NIH Common Fund Data Resources
PHAROS  P19544
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*CP*GP*C)-3')C11synthetic construct
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(1CC)P*GP*T)-3')B11synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.493α = 90
b = 77.211β = 90
c = 35.794γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM049245

Revision History 

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-09-21
    Changes: Database references
  • Version 1.2: 2016-12-14
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence
  • Version 2.0: 2020-06-24
    Changes: Atomic model