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Yorodumi- PDB-4l96: Structure of the complex between the F360L PPARgamma mutant and t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l96 | ||||||
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Title | Structure of the complex between the F360L PPARgamma mutant and the ligand LT175 (space group I222) | ||||||
Components | Peroxisome proliferator-activated receptor gamma | ||||||
Keywords | TRANSCRIPTION/TRANSCRIPTION inhibitor / transcription factor / RXRalpha / TRANSCRIPTION-TRANSCRIPTION inhibitor complex | ||||||
Function / homology | Function and homology information 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 / 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 / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonic acid binding ...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 / 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 / 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 / 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 / LBD domain binding / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / E-box binding / alpha-actinin binding / negative regulation of blood vessel endothelial cell migration / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / cellular response to low-density lipoprotein particle stimulus / positive regulation of cholesterol efflux / 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 / nuclear retinoid X receptor binding / negative regulation of signaling receptor activity / regulation of cellular response to insulin stimulus / cell maturation / positive regulation of adipose tissue development / epithelial cell differentiation / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / negative regulation of angiogenesis / response to nutrient / negative regulation of MAP kinase activity / fatty acid metabolic process / negative regulation of miRNA transcription / placenta development / Regulation of PTEN gene transcription / negative regulation of smooth muscle cell proliferation / transcription coregulator binding / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / mRNA transcription by RNA polymerase II / SUMOylation of intracellular receptors / regulation of circadian rhythm / lipid metabolic process / PPARA activates gene expression / regulation of blood pressure / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / activation of cysteine-type endopeptidase activity involved in apoptotic process / rhythmic process / protein self-association / nuclear receptor activity / positive regulation of DNA-binding transcription factor activity / glucose homeostasis / cellular response to hypoxia / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / sequence-specific DNA binding / nucleic acid binding / cell differentiation / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / intracellular membrane-bounded organelle / innate immune response / negative regulation of DNA-templated transcription / chromatin binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | Pochetti, G. / Montanari, R. / Capelli, D. / Chiaraluce, R. / Consalvi, V. / Pasquo, A. / Lori, C. / Laghezza, A. / Loiodice, F. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structural basis of the transactivation deficiency of the human PPAR gamma F360L mutant associated with familial partial lipodystrophy. Authors: Lori, C. / Pasquo, A. / Montanari, R. / Capelli, D. / Consalvi, V. / Chiaraluce, R. / Cervoni, L. / Loiodice, F. / Laghezza, A. / Aschi, M. / Giorgi, A. / Pochetti, G. #1: Journal: J.Med.Chem. / Year: 2008 Title: Crystal structure of the peroxisome proliferator-activated receptor gamma (PPARgamma) ligand binding domain complexed with a novel partial agonist: a new region of the hydrophobic pocket could ...Title: Crystal structure of the peroxisome proliferator-activated receptor gamma (PPARgamma) ligand binding domain complexed with a novel partial agonist: a new region of the hydrophobic pocket could be exploited for drug design. Authors: Montanari, R. / Saccoccia, F. / Scotti, E. / Crestani, M. / Godio, C. / Gilardi, F. / Loiodice, F. / Fracchiolla, G. / Laghezza, A. / Tortorella, P. / Lavecchia, A. / Novellino, E. / Mazza, ...Authors: Montanari, R. / Saccoccia, F. / Scotti, E. / Crestani, M. / Godio, C. / Gilardi, F. / Loiodice, F. / Fracchiolla, G. / Laghezza, A. / Tortorella, P. / Lavecchia, A. / Novellino, E. / Mazza, F. / Aschi, M. / Pochetti, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l96.cif.gz | 122.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l96.ent.gz | 95.2 KB | Display | PDB format |
PDBx/mmJSON format | 4l96.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/4l96 ftp://data.pdbj.org/pub/pdb/validation_reports/l9/4l96 | HTTPS FTP |
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-Related structure data
Related structure data | 4l98C 4o8fC 3b3kS S: Starting model for refinement C: citing same article (ref.) |
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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: 31376.473 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN (UNP RESIDUES 235-505) / Mutation: F360L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P37231 |
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#2: Chemical | ChemComp-LRG / ( |
#3: 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: 3.5 Å3/Da / Density % sol: 64.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 0.35M Na-phosphate, 0.65 M K-phosphate., pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.973 |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 1, 2013 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.973 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→50 Å / Num. all: 17959 / Num. obs: 17959 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.38→2.49 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 2.9 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3B3K Resolution: 2.38→80.84 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 12.49 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.65 Å2
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Refinement step | Cycle: LAST / Resolution: 2.38→80.84 Å
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