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- PDB-1k7l: The 2.5 Angstrom resolution crystal structure of the human PPARal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1k7l | ||||||
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Title | The 2.5 Angstrom resolution crystal structure of the human PPARalpha ligand binding domain bound with GW409544 and a co-activator peptide. | ||||||
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![]() | TRANSCRIPTION / The 2.5 Angstrom resolution crystal structure of the human PPARalpha ligand binding domain bound with GW409544 and a coactivator peptide | ||||||
Function / homology | ![]() positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / regulation of fatty acid metabolic process / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of fatty acid oxidation / cellular response to fructose stimulus / regulation of cellular ketone metabolic process / behavioral response to nicotine / negative regulation of appetite ...positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / regulation of fatty acid metabolic process / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of fatty acid oxidation / cellular response to fructose stimulus / regulation of cellular ketone metabolic process / 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 receptor 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 / DNA-binding transcription activator activity / hypothalamus development / positive regulation of fatty acid metabolic process / nitric oxide metabolic process / male mating behavior / positive regulation of ATP biosynthetic process / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NFAT protein binding / negative regulation of cholesterol storage / negative regulation of macrophage derived foam cell differentiation / cellular response to Thyroglobulin triiodothyronine / estrous cycle / Synthesis of bile acids and bile salts / negative regulation of cytokine production involved in inflammatory response / epidermis development / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / phosphatase binding / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / positive regulation of lipid biosynthetic process / nuclear retinoid X receptor binding / negative regulation of reactive oxygen species biosynthetic process / response to retinoic acid / histone acetyltransferase activity / regulation of cellular response to insulin stimulus / negative regulation of signaling receptor activity / Recycling of bile acids and salts / MDM2/MDM4 family protein binding / histone acetyltransferase / positive regulation of gluconeogenesis / 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 / RORA activates gene expression / negative regulation of blood pressure / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / cellular response to starvation / hormone-mediated signaling pathway / cerebellum development / response to nutrient / BMAL1:CLOCK,NPAS2 activates circadian gene expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / fatty acid metabolic process / gluconeogenesis / response to progesterone / hippocampus development / nuclear receptor binding / nuclear estrogen receptor binding / 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 / wound healing / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / response to insulin / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / transcription coactivator binding / 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 / nuclear receptor activity / male gonad development / Circadian Clock Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Xu, H.E. / Lambert, M.H. / Montana, V.G. / Moore, L.B. / Collins, J.L. / Oplinger, J.A. / Kliewer, S.A. / Gampe Jr., R.T. / McKee, D.D. / Moore, J.T. / Willson, T.M. | ||||||
![]() | ![]() Title: Structural determinants of ligand binding selectivity between the peroxisome proliferator-activated receptors. Authors: Xu, H.E. / Lambert, M.H. / Montana, V.G. / Plunket, K.D. / Moore, L.B. / Collins, J.L. / Oplinger, J.A. / Kliewer, S.A. / Gampe Jr., R.T. / McKee, D.D. / Moore, J.T. / Willson, T.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 236.2 KB | Display | ![]() |
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PDB format | ![]() | 191.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 653.7 KB | Display | ![]() |
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Full document | ![]() | 727.2 KB | Display | |
Data in XML | ![]() | 33.2 KB | Display | |
Data in CIF | ![]() | 48.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32731.014 Da / Num. of mol.: 4 / Fragment: ligand binding domain - residues 192 - 468 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 2431.750 Da / Num. of mol.: 4 / Fragment: src-1 peptide / Source method: obtained synthetically Details: Chemically synthesized 21mer portion of the the human src-1 coactivator peptide. References: UniProt: O43792, UniProt: Q15788*PLUS #3: Chemical | ChemComp-544 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.17 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 3350, NaNO3, hexanediol, YCl3, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 49991 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 52.8 Å2 / Rsym value: 0.054 |
Reflection | *PLUS Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS Mean I/σ(I) obs: 5.7 |
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Processing
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Refinement | Resolution: 2.5→19.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 318526.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 58.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor obs: 0.247 / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.247 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.365 / Rfactor Rwork: 0.308 |