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Yorodumi- PDB-7bpz: X-ray structure of human PPARalpha ligand binding domain-bezafibr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bpz | ||||||
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Title | X-ray structure of human PPARalpha ligand binding domain-bezafibrate-SRC1 coactivator peptide co-crystals obtained by soaking | ||||||
Components |
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Keywords | TRANSCRIPTION / Nuclear receptor / Protein-ligand complex / PPAR | ||||||
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 / labyrinthine layer morphogenesis / ubiquitin conjugating enzyme binding / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / negative regulation of glycolytic process / positive regulation of female receptivity / negative regulation of sequestering of triglyceride / nuclear steroid receptor activity / hypothalamus development / DNA-binding transcription activator activity / male mating behavior / positive regulation of fatty acid metabolic process / nitric oxide metabolic process / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / positive regulation of ATP biosynthetic process / NFAT protein binding / negative regulation of cholesterol storage / negative regulation of macrophage derived foam cell differentiation / estrous cycle / cellular response to Thyroglobulin triiodothyronine / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Synthesis of bile acids and bile salts / negative regulation of cytokine production involved in inflammatory response / epidermis development / phosphatase binding / MDM2/MDM4 family protein binding / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / positive regulation of lipid biosynthetic process / response to retinoic acid / negative regulation of signaling receptor activity / histone acetyltransferase activity / negative regulation of reactive oxygen species biosynthetic process / positive regulation of gluconeogenesis / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / negative regulation of blood pressure / RORA activates gene expression / lactation / cellular response to starvation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / cerebellum development / response to nutrient / BMAL1:CLOCK,NPAS2 activates circadian gene expression / fatty acid metabolic process / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / nuclear receptor coactivator activity / response to progesterone / gluconeogenesis / nuclear estrogen receptor binding / nuclear receptor binding / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / Heme signaling / response to insulin / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / wound healing / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / Circadian Clock Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.43 Å | ||||||
Authors | Kamata, S. / Ishikawa, R. / Akahane, M. / Oyama, T. / Ishii, I. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Iscience / Year: 2020 Title: PPAR alpha Ligand-Binding Domain Structures with Endogenous Fatty Acids and Fibrates. Authors: Kamata, S. / Oyama, T. / Saito, K. / Honda, A. / Yamamoto, Y. / Suda, K. / Ishikawa, R. / Itoh, T. / Watanabe, Y. / Shibata, T. / Uchida, K. / Suematsu, M. / Ishii, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bpz.cif.gz | 123.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bpz.ent.gz | 94.3 KB | Display | PDB format |
PDBx/mmJSON format | 7bpz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/7bpz ftp://data.pdbj.org/pub/pdb/validation_reports/bp/7bpz | HTTPS FTP |
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-Related structure data
Related structure data | 6kaxC 6kayC 6kazC 6kb0C 6kb1C 6kb2C 6kb3C 6kb4C 6kb5C 6kb6C 6kb7C 6kb8C 6kb9C 6kbaC 6kypC 6l36C 6l37C 6l38C 6lx4C 6lx5C 6lx6C 6lx7C 6lx8C 6lx9C 6lxaC 6lxbC 6lxcC 7bpyC 7bq0C 7bq1C 7bq2C 7bq3C 7bq4C 3sp6S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30856.053 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q07869 #2: Protein/peptide | Mass: 1848.177 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.8 Å3/Da / Density % sol: 56.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 0.1 M Tris (pH 8.5), 25 %(w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2020 / Details: Mirrors | |||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.43→46.74 Å / Num. obs: 27127 / % possible obs: 99.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 53.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.024 / Rrim(I) all: 0.044 / Net I/σ(I): 17.3 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SP6 Resolution: 2.43→36.068 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 28.99 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.68 Å2 / Biso mean: 62.7159 Å2 / Biso min: 35.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.43→36.068 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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