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Yorodumi- PDB-6onj: Crystal structure of PPARgamma ligand binding domain in complex w... -
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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 | ||||||
Components |
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Keywords | transcription/agonist / Nuclear receptors / TZDs / Drug design / Therapeutic targets / TRANSCRIPTION / transcription-agonist complex | ||||||
Function / homology | Function and homology information enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / mammary gland branching involved in thelarche / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / G0 to G1 transition / thyroid hormone mediated signaling pathway / core mediator complex ...enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / mammary gland branching involved in thelarche / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / G0 to G1 transition / thyroid hormone mediated signaling pathway / core mediator complex / regulation of vitamin D receptor signaling pathway / mediator complex / nuclear retinoic acid receptor binding / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / embryonic heart tube development / positive regulation of hepatocyte proliferation / cellular response to thyroid hormone stimulus / embryonic hindlimb morphogenesis / 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 / peroxisome proliferator activated receptor binding / nuclear vitamin D 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 / nuclear thyroid hormone receptor binding / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonic acid binding / embryonic hemopoiesis / positive regulation of low-density lipoprotein receptor activity / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / positive regulation of intracellular estrogen receptor signaling pathway / histone acetyltransferase binding / megakaryocyte development / erythrocyte development / positive regulation of vascular associated smooth muscle cell apoptotic process / macrophage derived foam cell differentiation / DNA binding domain binding / cellular response to hepatocyte growth factor stimulus / STAT family protein binding / positive regulation of fatty acid metabolic process / cellular response to steroid hormone stimulus / response to lipid / negative regulation of SMAD protein signal transduction / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / fat cell differentiation / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / E-box binding / alpha-actinin binding / negative regulation of blood vessel endothelial cell migration / lipid homeostasis / mammary gland branching involved in pregnancy / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / positive regulation of cholesterol efflux / negative regulation of macrophage derived foam cell differentiation / cellular response to low-density lipoprotein particle stimulus / negative regulation of lipid storage / 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 transcription initiation by RNA polymerase II / hematopoietic stem cell differentiation / positive regulation of fat cell differentiation / embryonic placenta development / negative regulation of keratinocyte proliferation / negative regulation of osteoblast differentiation / long-chain fatty acid transport / retinoic acid receptor signaling pathway / positive regulation of DNA binding / cell fate commitment / BMP signaling pathway / animal organ regeneration / ubiquitin ligase complex / nuclear retinoid X receptor binding / intracellular steroid hormone receptor signaling pathway / negative regulation of signaling receptor activity / RNA polymerase II preinitiation complex assembly / regulation of cellular response to insulin stimulus / cell maturation / keratinocyte differentiation / cellular response to epidermal growth factor stimulus / positive regulation of adipose tissue development / epithelial cell differentiation / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Shang, J. / Kojetin, D.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6onj.cif.gz | 72.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6onj.ent.gz | 52.2 KB | Display | PDB format |
PDBx/mmJSON format | 6onj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/6onj ftp://data.pdbj.org/pub/pdb/validation_reports/on/6onj | HTTPS FTP |
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-Related structure data
Related structure data | 6oniC 6pdzC 1prgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pET46 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37231 |
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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.) Homo sapiens (human) Gene: MED1, ARC205, CRSP1, CRSP200, DRIP205, DRIP230, PBP, PPARBP, PPARGBP, RB18A, TRAP220, TRIP2 Plasmid: pET46 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15648 |
#3: Chemical | ChemComp-BRL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
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: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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