6B0Q

Zinc finger Domain of WT1(-KTS form) with 13+1mer Oligonucleotide with 3' Triplet TGT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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, J.R.Zheng, Y.Blumenthal, R.M.Zhang, X.Cheng, X.

(2018) Nucleic Acids Res 46: 3864-3877

  • DOI: 10.1093/nar/gkx1274
  • Primary Citation of Related Structures:  
    6B0O, 6B0P, 6B0Q, 6B0R, 6BLW

  • PubMed Abstract: 
  • Wilms tumor protein (WT1) is a Cys2-His2 zinc-finger transcription factor vital for embryonic development of the genitourinary system. The protein contains a C-terminal DNA binding domain with four tandem zinc-fingers (ZF1-4). An alternative splicing of Wt1 can add three additional amino acids-lysine (K), threonine (T) and serine (S)-between ZF3 and ZF4 ...

    Wilms tumor protein (WT1) is a Cys2-His2 zinc-finger transcription factor vital for embryonic development of the genitourinary system. The protein contains a C-terminal DNA binding domain with four tandem zinc-fingers (ZF1-4). An alternative splicing of Wt1 can add three additional amino acids-lysine (K), threonine (T) and serine (S)-between ZF3 and ZF4. In the -KTS isoform, ZF2-4 determine the sequence-specificity of DNA binding, whereas the function of ZF1 remains elusive. Three X-ray structures are described here for wild-type -KTS isoform ZF1-4 in complex with its cognate DNA sequence. We observed four unique ZF1 conformations. First, like ZF2-4, ZF1 can be positioned continuously in the DNA major groove forming a 'near-cognate' complex. Second, while ZF2-4 make base-specific interactions with one DNA molecule, ZF1 can interact with a second DNA molecule (or, presumably, two regions of the same DNA molecule). Third, ZF1 can intercalate at the joint of two tail-to-head DNA molecules. If such intercalation occurs on a continuous DNA molecule, it would kink the DNA at the ZF1 binding site. Fourth, two ZF1 units can dimerize. Furthermore, we examined a Denys-Drash syndrome-associated ZF1 mutation (methionine at position 342 is replaced by arginine). This mutation enhances WT1 affinity for a guanine base. X-ray crystallography of the mutant in complex with its preferred sequence revealed the interactions responsible for this affinity change. These results provide insight into the mechanisms of action of WT1, and clarify the fact that ZF1 plays a role in determining sequence specificity of this critical transcription factor.


    Organizational Affiliation

    Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Wilms tumor proteinD [auth A],
A [auth D]
119Homo sapiensMutation(s): 0 
Gene Names: WT1
UniProt & NIH Common Fund Data Resources
Find proteins for P19544 (Homo sapiens)
Explore P19544 
Go to UniProtKB:  P19544
PHAROS:  P19544
GTEx:  ENSG00000184937 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19544
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*GP*CP*GP*TP*GP*GP*GP*AP*GP*TP*GP*TP*T)-3')E [auth B],
B [auth E]
14Homo sapiens
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*AP*AP*CP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')F [auth C],
C [auth F]
14Homo sapiens
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
K [auth D],
L [auth D],
M [auth D],
N [auth D],
S [auth A],
K [auth D],
L [auth D],
M [auth D],
N [auth D],
S [auth A],
T [auth A],
U [auth A],
V [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth D],
H [auth D],
I [auth D],
J [auth D],
O [auth A],
G [auth D],
H [auth D],
I [auth D],
J [auth D],
O [auth A],
P [auth A],
Q [auth A],
R [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.664α = 90
b = 161.664β = 90
c = 42.172γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-03
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Database references
  • Version 1.2: 2018-05-16
    Changes: Data collection, Database references