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Yorodumi- PDB-1i7g: CRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN FROM HUMAN PPAR-AL... -
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-Basic information
Entry | Database: PDB / ID: 1i7g | ||||||
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Title | CRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN FROM HUMAN PPAR-ALPHA IN COMPLEX WITH THE AGONIST AZ 242 | ||||||
Components | PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR ALPHA | ||||||
Keywords | TRANSCRIPTION / Anti parallel Helix Sandwich | ||||||
Function / homology | Function and homology information positive regulation of transformation of host cell by virus / regulation of fatty acid transport / regulation of fatty acid metabolic process / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of fatty acid oxidation / regulation of cellular ketone metabolic process / cellular response to fructose stimulus / behavioral response to nicotine / negative regulation of appetite ...positive regulation of transformation of host cell by virus / regulation of fatty acid transport / regulation of fatty acid metabolic process / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of fatty acid oxidation / regulation of cellular ketone metabolic process / cellular response to fructose stimulus / behavioral response to nicotine / negative regulation of appetite / positive regulation of fatty acid beta-oxidation / lipoprotein metabolic process / negative regulation of hepatocyte apoptotic process / mitogen-activated protein kinase kinase kinase binding / negative regulation of leukocyte cell-cell adhesion / ubiquitin conjugating enzyme binding / negative regulation of glycolytic process / negative regulation of sequestering of triglyceride / nuclear steroid receptor activity / DNA-binding transcription activator activity / positive regulation of fatty acid metabolic process / nitric oxide metabolic process / positive regulation of ATP biosynthetic process / NFAT protein binding / negative regulation of cholesterol storage / negative regulation of macrophage derived foam cell differentiation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of cytokine production involved in inflammatory response / epidermis development / phosphatase binding / MDM2/MDM4 family protein binding / positive regulation of lipid biosynthetic process / negative regulation of signaling receptor activity / negative regulation of reactive oxygen species biosynthetic process / positive regulation of gluconeogenesis / RORA activates gene expression / cellular response to starvation / negative regulation of blood pressure / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / response to nutrient / BMAL1:CLOCK,NPAS2 activates circadian gene expression / fatty acid metabolic process / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / gluconeogenesis / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / response to insulin / SUMOylation of intracellular receptors / Heme signaling / wound healing / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / nuclear receptor activity / Circadian Clock / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / cell differentiation / 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 / protein domain specific binding / lipid binding / chromatin / protein-containing complex binding / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Petersen, J.F.W. / Cronet, P. / Folmer, R. / Blomberg, N. / Sjoblom, K. / Karlsson, U. / Lindstedt, E.-L. / Bamberg, K. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Structure of the PPARalpha and -gamma ligand binding domain in complex with AZ 242; ligand selectivity and agonist activation in the PPAR family. Authors: Cronet, P. / Petersen, J.F. / Folmer, R. / Blomberg, N. / Sjoblom, K. / Karlsson, U. / Lindstedt, E.L. / Bamberg, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i7g.cif.gz | 69.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i7g.ent.gz | 49.2 KB | Display | PDB format |
PDBx/mmJSON format | 1i7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/1i7g ftp://data.pdbj.org/pub/pdb/validation_reports/i7/1i7g | HTTPS FTP |
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-Related structure data
Related structure data | 1i7iC 2prgS C: citing same article (ref.) 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: 32337.348 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q07869 |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-AZ2 / ( |
#4: Chemical | ChemComp-CPQ / |
#5: 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: 2.66 Å3/Da / Density % sol: 53.74 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: Sodium Formate, Hepes, DEOXY-BIGCHAP, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9465 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9465 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→30 Å / Num. obs: 17036 / % possible obs: 99.5 % / Redundancy: 5.2 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.24→2.39 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2 / % possible all: 99.7 |
Reflection | *PLUS Lowest resolution: 20 Å / Rmerge(I) obs: 0.062 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry: 2PRG A molecule Resolution: 2.2→23.64 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2276975.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 48.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→23.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.237 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.352 / % reflection Rfree: 5 % / Rfactor Rwork: 0.289 |