[English] 日本語
Yorodumi- PDB-2jp9: Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jp9 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to DNA | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION/DNA / DNA binding / nucleic acid recognition / residual dipolar coupling / zinc finger / Metal-binding / Zinc-finger / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information 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 ...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 / 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 / Transcriptional regulation of testis differentiation / gonad development / podocyte differentiation / cardiac muscle cell fate commitment / double-stranded methylated DNA binding / hemi-methylated DNA-binding / tissue development / male genitalia development / glomerulus development / camera-type eye development / C2H2 zinc finger domain binding / ureteric bud development / 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 / negative regulation of translation / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / positive regulation of gene expression / nucleolus / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / 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 | Homo sapiens (human) synthetic construct (others) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Stoll, R. / Lee, B.M. / Debler, E.W. / Laity, J.H. / Wilson, I.A. / Dyson, H.J. / Wright, P.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2jp9.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2jp9.ent.gz | 1001.6 KB | Display | PDB format |
PDBx/mmJSON format | 2jp9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/2jp9 ftp://data.pdbj.org/pub/pdb/validation_reports/jp/2jp9 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: DNA chain | Mass: 5261.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#2: DNA chain | Mass: 5159.327 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.) Homo sapiens (human) / Gene: WT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4VXV4, UniProt: P19544*PLUS |
#4: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 0.6 mM [U-100% 13C; U-100% 15N] wt1, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
---|---|
Sample | Conc.: 0.6 mM / Component: wt1 / 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 |
---|
-Processing
NMR software |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
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 |