[English] 日本語
Yorodumi- PDB-2zk6: Human peroxisome proliferator-activated receptor gamma ligand bin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zk6 | ||||||
---|---|---|---|---|---|---|---|
Title | Human peroxisome proliferator-activated receptor gamma ligand binding domain complexed with C8-BODIPY | ||||||
Components | Peroxisome proliferator-activated receptor gamma | ||||||
Keywords | TRANSCRIPTION / anti parallel helix sandwich / Activator / Diabetes mellitus / Disease mutation / DNA-binding / Metal-binding / Nucleus / Obesity / Phosphoprotein / Receptor / Transcription regulation / Zinc-finger | ||||||
Function / homology | Function and homology information prostaglandin receptor activity / regulation of cholesterol transporter activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonic acid binding ...prostaglandin receptor activity / regulation of cholesterol transporter activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonic acid binding / positive regulation of low-density lipoprotein receptor activity / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / DNA binding domain binding / macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / STAT family protein binding / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / LBD domain binding / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / E-box binding / alpha-actinin binding / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / negative regulation of blood vessel endothelial cell migration / cellular response to low-density lipoprotein particle stimulus / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of mitochondrial fission / positive regulation of cholesterol efflux / retinoic acid receptor signaling pathway / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / cell fate commitment / positive regulation of DNA binding / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / regulation of cellular response to insulin stimulus / negative regulation of signaling receptor activity / cell maturation / epithelial cell differentiation / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / negative regulation of angiogenesis / response to nutrient / negative regulation of miRNA transcription / negative regulation of MAP kinase activity / fatty acid metabolic process / Regulation of PTEN gene transcription / transcription coregulator binding / negative regulation of smooth muscle cell proliferation / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / placenta development / regulation of circadian rhythm / lipid metabolic process / PPARA activates gene expression / regulation of blood pressure / positive regulation of DNA-binding transcription factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / activation of cysteine-type endopeptidase activity involved in apoptotic process / nuclear receptor activity / : / rhythmic process / glucose homeostasis / cellular response to hypoxia / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / sequence-specific DNA binding / nucleic acid binding / cell differentiation / receptor complex / transcription cis-regulatory region binding / 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 gene expression / intracellular membrane-bounded organelle / innate immune response / negative regulation of DNA-templated transcription / chromatin binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | ||||||
Authors | Waku, T. / Shiraki, T. / Oyama, T. / Fujimoto, Y. / Morikawa, K. | ||||||
Citation | Journal: Embo J. / Year: 2010 Title: The nuclear receptor PPARgamma individually responds to serotonin- and fatty acid-metabolites Authors: Waku, T. / Shiraki, T. / Oyama, T. / Maebara, K. / Nakamori, R. / Morikawa, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2zk6.cif.gz | 119.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2zk6.ent.gz | 93.1 KB | Display | PDB format |
PDBx/mmJSON format | 2zk6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zk6_validation.pdf.gz | 887.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2zk6_full_validation.pdf.gz | 921.3 KB | Display | |
Data in XML | 2zk6_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 2zk6_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/2zk6 ftp://data.pdbj.org/pub/pdb/validation_reports/zk/2zk6 | HTTPS FTP |
-Related structure data
Related structure data | 3adsC 3adtC 3aduC 3advC 3adwC 3adxC 1prgS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32530.652 Da / Num. of mol.: 2 / Fragment: ligand binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: pparg / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P37231 #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | COMMON NAME OF C08 IS C8-BODIPY | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.46 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, 0.8M Sodium Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 11, 2007 |
Radiation | Monochromator: Fixed exit Si 111 double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 25325 / Num. obs: 24721 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 35.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.2 / Num. unique all: 2203 / % possible all: 88 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PRG Resolution: 2.41→48.76 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 200597.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.1099 Å2 / ksol: 0.35417 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.8 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.41→48.76 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.41→2.55 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|