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Yorodumi- PDB-8hul: X-ray structure of human PPAR delta ligand binding domain-lanifib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hul | ||||||||||||
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Title | X-ray structure of human PPAR delta ligand binding domain-lanifibranor co-crystals obtained by co-crystallization | ||||||||||||
Components | Peroxisome proliferator-activated receptor delta | ||||||||||||
Keywords | TRANSCRIPTION / Nuclear receptor / Protein-ligand complex / PPAR | ||||||||||||
Function / homology | Function and homology information fat cell proliferation / positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / glucose transmembrane transport / positive regulation of myoblast proliferation / fatty acid catabolic process ...fat cell proliferation / positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / glucose transmembrane transport / positive regulation of myoblast proliferation / fatty acid catabolic process / Carnitine metabolism / negative regulation of myoblast differentiation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / nuclear steroid receptor activity / positive regulation of fatty acid metabolic process / cell-substrate adhesion / fatty acid beta-oxidation / negative regulation of cholesterol storage / cellular response to nutrient levels / decidualization / keratinocyte proliferation / positive regulation of fat cell differentiation / fatty acid transport / adipose tissue development / energy homeostasis / embryo implantation / hormone-mediated signaling pathway / cholesterol metabolic process / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of miRNA transcription / fatty acid metabolic process / generation of precursor metabolites and energy / apoptotic signaling pathway / wound healing / lipid metabolic process / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / Nuclear Receptor transcription pathway / glucose metabolic process / nuclear receptor activity / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / cellular response to hypoxia / DNA-binding transcription factor binding / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / 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 DNA-templated transcription / lipid binding / apoptotic process / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / 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 / molecular replacement / Resolution: 2.461 Å | ||||||||||||
Authors | Kamata, S. / Honda, A. / Machida, Y. / Uchii, K. / Shiiyama, Y. / Masuda, R. / Oyama, T. / Ishii, I. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Antioxidants / Year: 2023 Title: Functional and Structural Insights into the Human PPAR alpha / delta / gamma Targeting Preferences of Anti-NASH Investigational Drugs, Lanifibranor, Seladelpar, and Elafibranor. Authors: Kamata, S. / Honda, A. / Ishikawa, R. / Akahane, M. / Fujita, A. / Kaneko, C. / Miyawaki, S. / Habu, Y. / Shiiyama, Y. / Uchii, K. / Machida, Y. / Oyama, T. / Ishii, I. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hul.cif.gz | 118.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hul.ent.gz | 90.4 KB | Display | PDB format |
PDBx/mmJSON format | 8hul.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hul_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8hul_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8hul_validation.xml.gz | 20 KB | Display | |
Data in CIF | 8hul_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/8hul ftp://data.pdbj.org/pub/pdb/validation_reports/hu/8hul | HTTPS FTP |
-Related structure data
Related structure data | 8hukC 8humC 8hunC 8huoC 8hupC 8huqC 7wglS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 31527.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPARD, NR1C2, PPARB / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q03181 #2: Chemical | 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: 2.83 Å3/Da / Density % sol: 56.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.05 M Bis-tris propane (pH 8.0), 14% PEG8000, 0.1 M KSCN, 6% propanediol, 0.001 M EDTA, 0.001 M CaCl2 |
-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: Jun 25, 2022 / 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: 2.46→48.02 Å / Num. obs: 25193 / % possible obs: 98.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 36.26 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.042 / Rrim(I) all: 0.079 / Net I/σ(I): 12.3 / Num. measured all: 87903 | |||||||||||||||||||||||||||
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: 7WGL Resolution: 2.461→38.805 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 28.26 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.24 Å2 / Biso mean: 41.6428 Å2 / Biso min: 14.93 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.461→38.805 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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