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Yorodumi- PDB-4pvu: Crystal structure of the complex between PPARgamma-LBD and the R ... -
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-Basic information
Entry | Database: PDB / ID: 4pvu | ||||||
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Title | Crystal structure of the complex between PPARgamma-LBD and the R enantiomer of Mbx-102 (Metaglidasen) | ||||||
Components | Peroxisome proliferator-activated receptor gamma | ||||||
Keywords | TRANSCRIPTION / ALPHA-HELICES / SMALL FOUR-STRANDED BETA-SHEET / ACTIVATOR / TDNA-BINDING / NUCLEUS / OBESITY / RECEPTOR / TRANSCRIPTION REGULATION | ||||||
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 / DNA binding domain binding / macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / 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 / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / negative regulation of macrophage derived foam cell differentiation / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of mitochondrial fission / positive regulation of cholesterol efflux / retinoic acid receptor signaling pathway / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / cell fate commitment / positive regulation of DNA binding / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / regulation of cellular response to insulin stimulus / cell maturation / negative regulation of signaling receptor activity / epithelial cell differentiation / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / negative regulation of angiogenesis / response to nutrient / negative regulation of miRNA transcription / negative regulation of MAP kinase activity / fatty acid metabolic process / Regulation of PTEN gene transcription / transcription coregulator binding / negative regulation of smooth muscle cell proliferation / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / placenta development / regulation of circadian rhythm / lipid metabolic process / PPARA activates gene expression / regulation of blood pressure / positive regulation of DNA-binding transcription factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / nuclear receptor activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / : / rhythmic process / 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: 2.6 Å | ||||||
Authors | Pochetti, G. / Montanari, R. / Capelli, D. / Loiodice, F. / Laghezza, A. / Piemontese, L. / Lavecchia, A. | ||||||
Citation | Journal: Chemmedchem / Year: 2015 Title: On the metabolically active form of metaglidasen: improved synthesis and investigation of its peculiar activity on peroxisome proliferator-activated receptors and skeletal muscles. Authors: Laghezza, A. / Montanari, R. / Lavecchia, A. / Piemontese, L. / Pochetti, G. / Iacobazzi, V. / Infantino, V. / Capelli, D. / De Bellis, M. / Liantonio, A. / Pierno, S. / Tortorella, P. / ...Authors: Laghezza, A. / Montanari, R. / Lavecchia, A. / Piemontese, L. / Pochetti, G. / Iacobazzi, V. / Infantino, V. / Capelli, D. / De Bellis, M. / Liantonio, A. / Pierno, S. / Tortorella, P. / Conte Camerino, D. / Loiodice, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pvu.cif.gz | 220.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pvu.ent.gz | 178.1 KB | Display | PDB format |
PDBx/mmJSON format | 4pvu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pvu_validation.pdf.gz | 690.3 KB | Display | wwPDB validaton report |
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Full document | 4pvu_full_validation.pdf.gz | 701.5 KB | Display | |
Data in XML | 4pvu_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 4pvu_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/4pvu ftp://data.pdbj.org/pub/pdb/validation_reports/pv/4pvu | HTTPS FTP |
-Related structure data
Related structure data | 4pwlC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 207 - 473 / Label seq-ID: 17 - 283
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-Components
#1: Protein | Mass: 32693.824 Da / Num. of mol.: 2 / Fragment: Ligand Binding Domain, UNP RESIDUES 223-505 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: peT28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P37231 #2: Chemical | ChemComp-MGZ / ( | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.8M Sodium Citrate, pH 8, 0.15M Tris, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2013 |
Radiation | Monochromator: Si 311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→115.82 Å / Num. all: 19580 / Num. obs: 19580 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2296 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3B3K Resolution: 2.6→57.91 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 29.418 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R: 0.74 / ESU R Free: 0.314 / 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: 87.355 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→57.91 Å
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