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- PDB-2jpa: 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: 2jpa | ||||||
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Title | Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to DNA | ||||||
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![]() | TRANSCRIPTION/DNA / DNA binding / nucleic acid recognition / residual dipolar coupling / zinc finger / Metal-binding / 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 | ![]() synthetic construct (others) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
![]() | 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 | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 941.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: DNA chain | Mass: 4353.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 4211.734 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#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: SOLUTION NMR | ||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 0.6 mM [U-100% 13C; U-100% 15N] wt1-14mer, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.6 mM / Component: wt1-14mer / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: 20 / pH: 6.7 / Pressure: ambient / Temperature: 310 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz |
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Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |