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Yorodumi- PDB-2i4j: Crystal structure of the complex between PPARgamma and the agonis... -
+Open data
-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) | ||||||
Components | Peroxisome proliferator-activated receptor gamma | ||||||
Keywords | TRANSCRIPTION / bundle of alpha-helices and a small four-stranded beta-sheet | ||||||
Function / homology | Function and homology information Complex I biogenesis / Respiratory electron transport / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / NADH dehydrogenase (ubiquinone) activity / mitochondrial membrane ...Complex I biogenesis / Respiratory electron transport / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / NADH dehydrogenase (ubiquinone) activity / mitochondrial membrane / aerobic respiration / mitochondrial inner membrane / mitochondrion / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å | ||||||
Authors | Pochetti, G. / Mazza, F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 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: Journal: Nature / Year: 1998 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: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i4j.cif.gz | 123.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i4j.ent.gz | 96.7 KB | Display | PDB format |
PDBx/mmJSON format | 2i4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2i4j_validation.pdf.gz | 710.9 KB | Display | wwPDB validaton report |
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Full document | 2i4j_full_validation.pdf.gz | 735.9 KB | Display | |
Data in XML | 2i4j_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 2i4j_validation.cif.gz | 35.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/2i4j ftp://data.pdbj.org/pub/pdb/validation_reports/i4/2i4j | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37231 #2: Chemical | ChemComp-DRJ / ( | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å |
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 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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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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