[English] 日本語
Yorodumi- PDB-4r2s: Wilms Tumor Protein (WT1) Q369P zinc fingers in complex with meth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r2s | ||||||
---|---|---|---|---|---|---|---|
Title | Wilms Tumor Protein (WT1) Q369P zinc fingers in complex with methylated DNA | ||||||
Components |
| ||||||
Keywords | DNA Binding Protein/DNA / Zinc finger / Transcription / DNA Binding Protein-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 / 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 / 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 / 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 / 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 / regulation of DNA-templated transcription / nucleolus / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.489 Å | ||||||
Authors | Hashimoto, H. / Olanrewaju, Y.O. / Zheng, Y. / Wilson, G.G. / Zhang, X. / Cheng, X. | ||||||
Citation | Journal: Genes Dev. / Year: 2014 Title: Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence. Authors: Hashimoto, H. / Olanrewaju, Y.O. / Zheng, Y. / Wilson, G.G. / Zhang, X. / Cheng, X. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4r2s.cif.gz | 49 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4r2s.ent.gz | 30.6 KB | Display | PDB format |
PDBx/mmJSON format | 4r2s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r2s_validation.pdf.gz | 446.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4r2s_full_validation.pdf.gz | 446.1 KB | Display | |
Data in XML | 4r2s_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 4r2s_validation.cif.gz | 8.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/4r2s ftp://data.pdbj.org/pub/pdb/validation_reports/r2/4r2s | HTTPS FTP |
-Related structure data
Related structure data | 4r2aC 4r2cC 4r2dC 4r2eSC 4r2pC 4r2qC 4r2rC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 11251.867 Da / Num. of mol.: 1 / Fragment: Zinc Finger 2-4 / Mutation: Q369P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WT1 / Plasmid: pGEX6p-1, pXC1303 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: P19544 |
---|
-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 3444.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) synthetic construct (others) |
---|---|
#3: DNA chain | Mass: 3293.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 30 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.61 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 12% (w/v) PEG 3350, 0.1 M Ammonium Citrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 9, 2014 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.489→29.4 Å / Num. all: 5690 / Num. obs: 5690 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 38.88 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2.49→2.58 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 6.6 / Num. unique all: 545 / % possible all: 92.1 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4R2E Resolution: 2.489→29.361 Å / SU ML: 0.29 / σ(F): 1.36 / Phase error: 29.62 / Stereochemistry target values: ML
| |||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.489→29.361 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION
|