Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.17 kDa 
• Atom Count: 1712 
• Residue Count: 153 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

2JP9

Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to DNA

• DOI: 10.2210/pdb2JP9/pdb
• NDB: 2JP9
• BMRB: 15532

• Classification: TRANSCRIPTION/DNA
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-30 Released: 2007-10-30 
• Deposition Author(s): Stoll, R., Lee, B.M., Debler, E.W., Laity, J.H., Wilson, I.A., Dyson, H.J., Wright, P.E.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Structure of the wilms tumor suppressor protein zinc finger domain bound to DNA

Stoll, R., Lee, B.M., Debler, E.W., Laity, J.H., Wilson, I.A., Dyson, H.J., Wright, P.E.

(2007) J Mol Biol 372: 1227-1245

• PubMed: 17716689 
• DOI: 10.1016/j.jmb.2007.07.017
• Primary Citation of Related Structures:  
  2PRT, 2JP9, 2JPA


• PubMed Abstract: 
  

The zinc finger domain of the Wilms tumor suppressor protein (WT1) contains four canonical Cys(2)His(2) zinc fingers. WT1 binds preferentially to DNA sequences that are closely related to the EGR-1 consensus site. We report the structure determination by both X-ray crystallography and NMR spectroscopy of the WT1 zinc finger domain in complex with DNA. The X-ray structure was determined for the complex with a cognate 14 base-pair oligonucleotide, and composite X-ray/NMR structures were determined for complexes with both the 14 base-pair and an extended 17 base-pair DNA. This combined approach allowed unambiguous determination of the position of the first zinc finger, which is influenced by lattice contacts in the crystal structure. The crystal structure shows the second, third and fourth zinc finger domains inserted deep into the major groove of the DNA where they make base-specific interactions. The DNA duplex is distorted in the vicinity of the first zinc finger, with a cytidine twisted and tilted out of the base stack to pack against finger 1 and the tip of finger 2. By contrast, the composite X-ray/NMR structures show that finger 1 continues to follow the major groove in the solution complexes. However, the orientation of the helix is non-canonical, and the fingertip and the N terminus of the helix project out of the major groove; as a consequence, the zinc finger side-chains that are commonly involved in base recognition make no contact with the DNA. We conclude that finger 1 helps to anchor WT1 to the DNA by amplifying the binding affinity although it does not contribute significantly to binding specificity. The structures provide molecular level insights into the potential consequences of mutations in zinc fingers 2 and 3 that are associated with Denys-Drash syndrome and nephritic syndrome. The mutations are of two types, and either destabilize the zinc finger structure or replace key base contact residues.

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Organizational Affiliation: 

Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Wilms tumor 1	A	119	Homo sapiens	Mutation(s): 0  Gene Names: WT1
Find proteins for P19544 (Homo sapiens) Explore P19544  Go to UniProtKB:  P19544
NIH Common Fund Data Resources
PHAROS  P19544 GTEx  ENSG00000184937

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*DCP*DGP*DCP*DGP*DGP*DGP*DGP*DGP*DCP*DGP*DTP*DCP*DTP*DGP*DCP*DGP*DC)-3')	B	17	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*DGP*DCP*DGP*DCP*DAP*DGP*DAP*DCP*DGP*DCP*DCP*DCP*DCP*DCP*DGP*DCP*DG)-3')	C	17	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2JP9 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-04-30 
• Released Date: 2007-10-30 
Deposition Author(s): Stoll, R., Lee, B.M., Debler, E.W., Laity, J.H., Wilson, I.A., Dyson, H.J., Wright, P.E.

Revision History 

• Version 1.0: 2007-10-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-02-05
  Changes: Data collection, Database references, Derived calculations, Other, Source and taxonomy