[English] 日本語
![](img/lk-miru.gif)
- PDB-4r2q: Wilms Tumor Protein (WT1) zinc fingers in complex with formylated DNA -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4r2q | ||||||
---|---|---|---|---|---|---|---|
Title | Wilms Tumor Protein (WT1) zinc fingers in complex with formylated DNA | ||||||
![]() |
| ||||||
![]() | DNA Binding Protein/DNA / Zinc finger / Transcription / DNA Binding Protein-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 | ![]() ![]() ![]() | ||||||
![]() | Hashimoto, H. / Olanrewaju, Y.O. / Zheng, Y. / Wilson, G.G. / Zhang, X. / Cheng, X. | ||||||
![]() | ![]() 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: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 88.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 63.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4r2aC ![]() 4r2cC ![]() 4r2dC ![]() 4r2eSC ![]() 4r2pC ![]() 4r2rC ![]() 4r2sC C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 11282.882 Da / Num. of mol.: 1 / Fragment: Zinc Finger 2-4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 3458.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) synthetic construct (others) |
---|---|
#3: DNA chain | Mass: 3307.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 185 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.9 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 12% (w/v) PEG 3350, 4% (v/v) Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 12, 2013 |
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: 1.54→19.447 Å / Num. obs: 28341 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 18.34 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.54→1.6 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2798 / % possible all: 99.9 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4R2E Resolution: 1.54→19.447 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 18.62 / 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: 1.54→19.447 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION
|