+
Open data
-
Basic information
Entry | Database: PDB / ID: 4r2a | ||||||
---|---|---|---|---|---|---|---|
Title | Egr1/Zif268 zinc fingers in complex with methylated DNA | ||||||
![]() |
| ||||||
![]() | DNA Binding Protein/DNA / Zinc finger / Transcription / DNA Binding Protein-DNA complex | ||||||
Function / homology | ![]() glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / regulation of protein sumoylation / cellular response to heparin / cellular response to mycophenolic acid / circadian temperature homeostasis / positive regulation of post-translational protein modification / positive regulation of hormone biosynthetic process ...glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / regulation of protein sumoylation / cellular response to heparin / cellular response to mycophenolic acid / circadian temperature homeostasis / positive regulation of post-translational protein modification / positive regulation of hormone biosynthetic process / double-stranded methylated DNA binding / hemi-methylated DNA-binding / positive regulation of gene expression via chromosomal CpG island demethylation / NGF-stimulated transcription / interleukin-1-mediated signaling pathway / histone acetyltransferase binding / skeletal muscle cell differentiation / locomotor rhythm / T cell differentiation / estrous cycle / BMP signaling pathway / regulation of neuron apoptotic process / response to glucose / positive regulation of chemokine production / positive regulation of interleukin-1 beta production / Regulation of PTEN gene transcription / response to ischemia / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / response to insulin / negative regulation of canonical Wnt signaling pathway / cellular response to gamma radiation / positive regulation of miRNA transcription / sequence-specific double-stranded DNA binding / Interferon alpha/beta signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / 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 | ![]() | 84.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 60 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 449.2 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 12.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4r2cC ![]() 4r2dC ![]() 4r2eC ![]() 4r2pC ![]() 4r2qC ![]() 4r2rC ![]() 4r2sC ![]() 1aayS 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: 11133.757 Da / Num. of mol.: 1 / Fragment: Zinc Finger 1-3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-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, 187 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.38 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 12% (v/v) PEG 3350, 4% 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 7, 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: 1.59→28.104 Å / Num. obs: 21919 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 28.895 |
Reflection shell | Resolution: 1.59→1.65 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2098 / % possible all: 95.8 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1AAY Resolution: 1.591→28.104 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 18.12 / 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: 1.591→28.104 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION
|