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- PDB-2i4j: Crystal structure of the complex between PPARgamma and the agonis... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2i4j | ||||||
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Title | Crystal structure of the complex between PPARgamma and the agonist LT160 (ureidofibrate derivative) | ||||||
![]() | Peroxisome proliferator-activated receptor gamma | ||||||
![]() | TRANSCRIPTION / bundle of alpha-helices and a small four-stranded beta-sheet | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pochetti, G. / Mazza, F. | ||||||
![]() | ![]() Title: Insights into the mechanism of partial agonism: crystal structures of the peroxisome proliferator-activated receptor gamma ligand-binding domain in the complex with two enantiomeric ligands Authors: Pochetti, G. / Godio, C. / Mitro, N. / Caruso, D. / Galmozzi, A. / Scurati, S. / Loiodice, F. / Fracchiolla, G. / Tortorella, P. / Laghezza, A. / Lavecchia, A. / Novellino, E. / Mazza, F. / Crestani, M. #1: ![]() Title: Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-gamma Authors: Nolte, R.T. / Wisely, G.B. / Westin, S. / Cobb, J.E. / Lambert, M.H. / Kurokawa, R. / Rosenfeld, M.G. / Willson, T.M. / Glass, C.K. / Milburn, M.V. #2: ![]() Title: A peroxisome proliferator-activated receptor gamma ligand inhibits adipocyte differentiation Authors: Oberfield, J.L. / Collins, J.L. / Holmes, C.P. / Goreham, D.M. / Cooper, J.P. / Cobb, J.E. / Lenhard, J.M. / Hull-Ryde, E.A. / Mohr, C.P. / Blanchard, S.G. / Parks, D.J. / Moore, L.B. / ...Authors: Oberfield, J.L. / Collins, J.L. / Holmes, C.P. / Goreham, D.M. / Cooper, J.P. / Cobb, J.E. / Lenhard, J.M. / Hull-Ryde, E.A. / Mohr, C.P. / Blanchard, S.G. / Parks, D.J. / Moore, L.B. / Lehmann, J.M. / Plunket, K. / Miller, A.B. / Milburn, M.V. / Kliewer, S.A. / 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 | ![]() | 123.9 KB | Display | ![]() |
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PDB format | ![]() | 96.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 710.9 KB | Display | ![]() |
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Full document | ![]() | 735.9 KB | Display | |
Data in XML | ![]() | 25.5 KB | Display | |
Data in CIF | ![]() | 35.3 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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Unit cell |
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Components
#1: Protein | Mass: 32530.652 Da / Num. of mol.: 2 / Fragment: ligand binding domain (LBD), residues 223-504 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-DRJ / ( | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.8 M NaCitrate, 0.15 M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 24, 2005 |
Radiation | Monochromator: double crystal monochromator (Si 111 and Si220) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 32657 / Num. obs: 32657 / % possible obs: 85.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rsym value: 0.04 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 2933 / Rsym value: 0.385 / % possible all: 77.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Bsol: 92.346 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.343 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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Xplor file |
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