[English] 日本語
![](img/lk-miru.gif)
- PDB-3v9v: Crystal structure of the PPARgamma-LBD complexed with a cercospor... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3v9v | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the PPARgamma-LBD complexed with a cercosporamide derivative modulator | ||||||
![]() |
| ||||||
![]() | TRANSCRIPTION/TRANSCRIPTION REGULATOR / three-layered alpha-helical sandwich / transcription regulation / TRANSCRIPTION-TRANSCRIPTION REGULATOR complex | ||||||
Function / homology | ![]() Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cellular respiration / lncRNA binding / digestion / temperature homeostasis / response to starvation / intracellular glucose homeostasis ...Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cellular respiration / lncRNA binding / digestion / temperature homeostasis / response to starvation / intracellular glucose homeostasis / fatty acid oxidation / response to dietary excess / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Complex I biogenesis / adipose tissue development / Respiratory electron transport / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / brown fat cell differentiation / mitochondrial ATP synthesis coupled electron transport / energy homeostasis / transcription coregulator activity / mitochondrial respiratory chain complex I assembly / positive regulation of gluconeogenesis / respiratory electron transport chain / RNA splicing / negative regulation of smooth muscle cell proliferation / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / : / mitochondrion organization / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / gluconeogenesis / nuclear receptor binding / NADH dehydrogenase (ubiquinone) activity / regulation of circadian rhythm / transcription initiation at RNA polymerase II promoter / PPARA activates gene expression / positive regulation of DNA-binding transcription factor activity / circadian regulation of gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / mitochondrial membrane / aerobic respiration / PML body / chromatin DNA binding / mRNA processing / Regulation of RUNX2 expression and activity / Circadian Clock / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / DNA-binding transcription factor binding / protein-containing complex assembly / neuron apoptotic process / sequence-specific DNA binding / transcription coactivator activity / negative regulation of neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / protein stabilization / mitochondrial inner membrane / ubiquitin protein ligase binding / positive regulation of gene expression / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Matsui, Y. / Hanzawa, H. | ||||||
![]() | ![]() Title: Substituents at the naphthalene C3 position of (-)-Cercosporamide derivatives significantly affect the maximal efficacy as PPAR(gamma) partial agonists Authors: Furukawa, A. / Arita, T. / Fukuzaki, T. / Satoh, S. / Mori, M. / Honda, T. / Matsui, Y. / Wakabayashi, K. / Hayashi, S. / Araki, K. / Ohsumi, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 72.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 52.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 733 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 738 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3v9tC ![]() 3v9yC ![]() 3lmpS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 32412.576 Da / Num. of mol.: 1 / Fragment: ligand binding domain, UNP residues 234-505 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Protein/peptide | Mass: 2067.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Chemical | ChemComp-21L / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.88 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, sodium thiocyanate, Tris-hydrochloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 93 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 8, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 36814 / Num. obs: 36676 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.066 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.3 % / Num. unique all: 3644 / % possible all: 99.9 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3LMP Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.929 / SU B: 1.91 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.196 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
|