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Yorodumi- PDB-3b1m: Crystal structure of the PPARgamma-LBD complexed with a cercospor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b1m | ||||||
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Title | Crystal structure of the PPARgamma-LBD complexed with a cercosporamide derivative modulator Cerco-A | ||||||
Components |
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Keywords | TRANSCRIPTION | ||||||
Function / homology | Function and homology information positive regulation of mitochondrial DNA metabolic process / positive regulation of muscle tissue development / positive regulation of cellular respiration / positive regulation of fatty acid oxidation / : / : / lncRNA binding / cellular respiration / prostaglandin receptor activity / regulation of cholesterol transporter activity ...positive regulation of mitochondrial DNA metabolic process / positive regulation of muscle tissue development / positive regulation of cellular respiration / positive regulation of fatty acid oxidation / : / : / lncRNA binding / cellular respiration / prostaglandin receptor activity / regulation of cholesterol transporter activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / response to muscle activity / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / negative regulation of cellular response to transforming growth factor beta stimulus / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonic acid binding / positive regulation of low-density lipoprotein receptor activity / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / temperature homeostasis / positive regulation of vascular associated smooth muscle cell apoptotic process / macrophage derived foam cell differentiation / DNA binding domain binding / STAT family protein binding / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / positive regulation of ATP biosynthetic process / response to starvation / LBD domain binding / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / response to dietary excess / E-box binding / alpha-actinin binding / negative regulation of blood vessel endothelial cell migration / lipid homeostasis / intracellular glucose homeostasis / fatty acid oxidation / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / positive regulation of cholesterol efflux / cellular response to low-density lipoprotein particle stimulus / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / long-chain fatty acid transport / retinoic acid receptor signaling pathway / positive regulation of DNA binding / cell fate commitment / BMP signaling pathway / adipose tissue development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / nuclear retinoid X receptor binding / energy homeostasis / brown fat cell differentiation / negative regulation of signaling receptor activity / regulation of cellular response to insulin stimulus / cell maturation / positive regulation of gluconeogenesis / digestion / positive regulation of adipose tissue development / epithelial cell differentiation / peroxisome proliferator activated receptor signaling pathway / mitochondrion organization / respiratory electron transport chain / hormone-mediated signaling pathway / negative regulation of angiogenesis / response to nutrient / negative regulation of MAP kinase activity / RNA splicing / fatty acid metabolic process / nuclear receptor coactivator activity / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / placenta development / Regulation of PTEN gene transcription / negative regulation of smooth muscle cell proliferation / gluconeogenesis / transcription coregulator binding / transcription initiation at RNA polymerase II promoter / nuclear receptor binding / transcription coregulator activity / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Matsui, Y. / Hiroyuki, H. | ||||||
Citation | Journal: Biol.Pharm.Bull. / Year: 2011 Title: Pharmacology and in Vitro Profiling of a Novel Peroxisome Proliferator-Activated Receptor gamma Ligand, Cerco-A Authors: Wakabayashi, K. / Hayashi, S. / Matsui, Y. / Matsumoto, T. / Furukawa, A. / Kuroha, M. / Tanaka, N. / Inaba, T. / Kanda, S. / Tanaka, J. / Okuyama, R. / Wakimoto, S. / Ogata, T. / Araki, K. / Ohsumi, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b1m.cif.gz | 75.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b1m.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 3b1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/3b1m ftp://data.pdbj.org/pub/pdb/validation_reports/b1/3b1m | HTTPS FTP |
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-Related structure data
Related structure data | 3lmpS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / References: UniProt: P37231 |
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#2: Protein/peptide | Mass: 2067.381 Da / Num. of mol.: 1 Fragment: peptide containing LXXLL box, UNP residues 136-154 Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2 |
#3: Chemical | ChemComp-KRC / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.25 % |
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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 |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jun 28, 2005 |
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: 37106 / Num. obs: 36868 / % possible obs: 99.4 % / Biso Wilson estimate: 22.8 Å2 / Rsym value: 0.055 |
Reflection shell | Resolution: 1.6→1.66 Å / Mean I/σ(I) obs: 4.25 / Num. unique all: 3530 / Rsym value: 0.255 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3LMP Resolution: 1.6→19 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 867084.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.0583 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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