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- PDB-6onj: Crystal structure of PPARgamma ligand binding domain in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6onj | ||||||
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Title | Crystal structure of PPARgamma ligand binding domain in complex with TRAP220 peptide and agonist rosiglitazone | ||||||
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![]() | transcription/agonist / Nuclear receptors / TZDs / Drug design / Therapeutic targets / TRANSCRIPTION / transcription-agonist complex | ||||||
Function / homology | ![]() enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / mammary gland branching involved in thelarche / G0 to G1 transition / thyroid hormone receptor signaling pathway / core mediator complex ...enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / mammary gland branching involved in thelarche / G0 to G1 transition / thyroid hormone receptor signaling pathway / core mediator complex / regulation of vitamin D receptor signaling pathway / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / nuclear retinoic acid receptor binding / mediator complex / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / embryonic heart tube development / cellular response to thyroid hormone stimulus / positive regulation of hepatocyte proliferation / prostaglandin receptor activity / embryonic hindlimb morphogenesis / 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 / nuclear vitamin D receptor binding / peroxisome proliferator activated receptor binding / 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 / lens development in camera-type eye / negative regulation of cardiac muscle hypertrophy in response to stress / positive regulation of intracellular estrogen receptor signaling pathway / arachidonic acid binding / positive regulation of low-density lipoprotein receptor activity / embryonic hemopoiesis / nuclear thyroid hormone receptor binding / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / DNA binding domain binding / megakaryocyte development / macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / STAT family protein binding / histone acetyltransferase binding / cellular response to steroid hormone stimulus / cellular response to hepatocyte growth factor stimulus / positive regulation of fatty acid metabolic process / response to lipid / RSV-host interactions / negative regulation of SMAD protein signal transduction / LBD domain binding / epithelial cell proliferation involved in mammary gland duct elongation / negative regulation of type II interferon-mediated signaling pathway / fat cell differentiation / negative regulation of cholesterol storage / E-box binding / alpha-actinin binding / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / mammary gland branching involved in pregnancy / R-SMAD binding / monocyte differentiation / negative regulation of macrophage derived foam cell differentiation / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / general transcription initiation factor binding / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of neuron differentiation / negative regulation of mitochondrial fission / positive regulation of cholesterol efflux / hematopoietic stem cell differentiation / embryonic placenta development / negative regulation of keratinocyte proliferation / retinoic acid receptor signaling pathway / positive regulation of transcription initiation by RNA polymerase II / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / cell fate commitment / positive regulation of DNA binding / animal organ regeneration / erythrocyte development / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone signaling pathway / ubiquitin ligase complex / RNA polymerase II preinitiation complex assembly / regulation of cellular response to insulin stimulus / keratinocyte differentiation / cell maturation / negative regulation of signaling receptor activity / cellular response to epidermal growth factor stimulus / epithelial cell differentiation / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Shang, J. / Kojetin, D.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A molecular switch regulating transcriptional repression and activation of PPAR gamma. Authors: Shang, J. / Mosure, S.A. / Zheng, J. / Brust, R. / Bass, J. / Nichols, A. / Solt, L.A. / Griffin, P.R. / Kojetin, D.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.8 KB | Display | ![]() |
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PDB format | ![]() | 52.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 330.7 KB | Display | ![]() |
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Full document | ![]() | 331.3 KB | Display | |
Data in XML | ![]() | 1.6 KB | Display | |
Data in CIF | ![]() | 5.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6oniC ![]() 6pdzC ![]() 1prgS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 31449.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 2197.513 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MED1, ARC205, CRSP1, CRSP200, DRIP205, DRIP230, PBP, PPARBP, PPARGBP, RB18A, TRAP220, TRIP2 Plasmid: pET46 / Production host: ![]() ![]() |
#3: Chemical | ChemComp-BRL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Sodium acetate trihydrate 0.1M Tris, pH 8.5 30% w/v, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 200 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2019 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→36.64 Å / Num. obs: 12926 / % possible obs: 99.6 % / Redundancy: 2 % / Biso Wilson estimate: 22.96 Å2 / Rmerge(I) obs: 0.023 / Net I/σ(I): 16.54 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 4.37 / Num. unique obs: 1260 / % possible all: 99.8 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PRG Resolution: 2.3→36.64 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.18 Å2 / Biso mean: 31.11 Å2 / Biso min: 8.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→36.64 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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