[English] 日本語
![](img/lk-miru.gif)
- PDB-7bq4: X-ray structure of human PPARalpha ligand binding domain-eicosape... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7bq4 | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of human PPARalpha ligand binding domain-eicosapentaenoic acid (EPA)-SRC1 coactivator peptide co-crystals obtained by delipidation and co-crystallization | ||||||
![]() |
| ||||||
![]() | TRANSCRIPTION / Nuclear receptor / Protein-ligand complex / PPAR | ||||||
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 / nitric oxide metabolic process / positive regulation of fatty acid 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 / phosphatase binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 / Recycling of bile acids and salts / negative regulation of signaling receptor activity / histone acetyltransferase / MDM2/MDM4 family protein binding / cellular response to hormone stimulus / positive regulation of gluconeogenesis / 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 estrogen receptor binding / nuclear 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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Kamata, S. / Ishikawa, R. / Akahane, M. / Oyama, T. / Ishii, I. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 75 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 52.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 687.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 690 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 17.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 ![]() 7bpzC ![]() 7bq0C ![]() 7bq1C ![]() 7bq2C ![]() 7bq3C ![]() 3sp6S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 30856.053 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Protein/peptide | Mass: 1848.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Chemical | ChemComp-EPA / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.79 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 0.1 M Tris (pH 8.0), 30 %(w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
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: 1.62→43.06 Å / Num. obs: 34634 / % possible obs: 98.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.73 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.021 / Rrim(I) all: 0.04 / Net I/σ(I): 19.3 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.2 %
|
-Phasing
Phasing | Method: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3SP6 Resolution: 1.62→39.189 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 21.13 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.63 Å2 / Biso mean: 22.7557 Å2 / Biso min: 10.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.62→39.189 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|