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- PDB-2prt: Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domai... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2prt | ||||||
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Title | Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to DNA | ||||||
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![]() | TRANSCRIPTION/DNA / Protein-DNA complex / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | ![]() posterior mesonephric tubule development / negative regulation of metanephric glomerular mesangial cell proliferation / positive regulation of metanephric ureteric bud development / thorax and anterior abdomen determination / metanephric epithelium development / regulation of animal organ formation / adrenal cortex formation / negative regulation of female gonad development / positive regulation of heart growth / visceral serous pericardium development ...posterior mesonephric tubule development / negative regulation of metanephric glomerular mesangial cell proliferation / positive regulation of metanephric ureteric bud development / thorax and anterior abdomen determination / metanephric epithelium development / regulation of animal organ formation / adrenal cortex formation / negative regulation of female gonad development / positive regulation of heart growth / visceral serous pericardium development / Nephron development / glomerular basement membrane development / diaphragm development / sex determination / mesenchymal to epithelial transition / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / positive regulation of male gonad development / cellular response to gonadotropin stimulus / gonad development / Transcriptional regulation of testis differentiation / podocyte differentiation / cardiac muscle cell fate commitment / double-stranded methylated DNA binding / tissue development / hemi-methylated DNA-binding / male genitalia development / glomerulus development / camera-type eye development / C2H2 zinc finger domain binding / ureteric bud development / negative regulation of gene expression via chromosomal CpG island methylation / branching involved in ureteric bud morphogenesis / adrenal gland development / germ cell development / vasculogenesis / cellular response to cAMP / epithelial cell differentiation / RNA splicing / kidney development / negative regulation of cell growth / positive regulation of miRNA transcription / male gonad development / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / negative regulation of translation / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / nuclear speck / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / nucleolus / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stoll, R. / Lee, B.M. / Debler, E.W. / Laity, J.H. / Wilson, I.A. / Dyson, H.J. / Wright, P.E. | ||||||
![]() | ![]() Title: Structure of the Wilms tumor suppressor protein zinc finger domain bound to DNA Authors: Stoll, R. / Lee, B.M. / Debler, E.W. / Laity, J.H. / Wilson, I.A. / Dyson, H.J. / Wright, P.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.6 KB | Display | ![]() |
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PDB format | ![]() | 33.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2jp9C ![]() 2jpaC ![]() 1aayS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 4353.801 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4211.734 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 14488.708 Da / Num. of mol.: 1 / Fragment: residues 174-291 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.97 Å3/Da / Density % sol: 69.04 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 6.7 Details: 10 mM d11-Tris/HCl, 20 mM KCl, 5uM ZnSO4, 2mM NaN3, 10% D2O, pH 6.7, SMALL TUBES, temperature 277K, pH 6.70 | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 97 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Feb 1, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1921 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→42.8 Å / Num. obs: 7166 / % possible obs: 99.1 % / Redundancy: 11.2 % / Rsym value: 0.085 / Net I/σ(I): 22.9 |
Reflection shell | Highest resolution: 3.15 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 5.3 / Rsym value: 0.435 / % possible all: 100 |
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Processing
Software | Name: CNS / Classification: refinement | ||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1AAY Highest resolution: 3.15 Å
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Refinement step | Cycle: LAST / Highest resolution: 3.15 Å
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LS refinement shell | Highest resolution: 3.15 Å / Rfactor Rfree: 0.405 / Rfactor Rwork: 0.376 |