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- PDB-7qaa: Crystal structure of RARalpha/RXRalpha ligand binding domain hete... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qaa | ||||||
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Title | Crystal structure of RARalpha/RXRalpha ligand binding domain heterodimer in complex with BMS614 and oleic acid | ||||||
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Function / homology | ![]() Transcriptional regulation of granulopoiesis / Carnitine metabolism / Transcriptional regulation of white adipocyte differentiation / Regulation of pyruvate dehydrogenase (PDH) complex / Sertoli cell fate commitment / Signaling by Retinoic Acid / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of binding / SUMOylation of intracellular receptors ...Transcriptional regulation of granulopoiesis / Carnitine metabolism / Transcriptional regulation of white adipocyte differentiation / Regulation of pyruvate dehydrogenase (PDH) complex / Sertoli cell fate commitment / Signaling by Retinoic Acid / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of binding / SUMOylation of intracellular receptors / trachea cartilage development / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / Nuclear Receptor transcription pathway / ventricular cardiac muscle cell differentiation / visceral serous pericardium development / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / mesenchyme development / chondroblast differentiation / positive regulation of translational initiation by iron / Endogenous sterols / embryonic camera-type eye development / glandular epithelial cell development / maternal placenta development / negative regulation of granulocyte differentiation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | le Maire, A. / Vivat, V. / Guee, L. / Blanc, P. / Malosse, C. / Chamot-Rooke, J. / Germain, P. / Bourguet, w. | ||||||
Funding support | 1items
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![]() | ![]() Title: Design and in vitro characterization of RXR variants as tools to investigate the biological role of endogenous rexinoids. Authors: le Maire, A. / Rey, M. / Vivat, V. / Guee, L. / Blanc, P. / Malosse, C. / Chamot-Rooke, J. / Germain, P. / Bourguet, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.4 KB | Display | ![]() |
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PDB format | ![]() | 79.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7pdqC ![]() 7pdtC ![]() 1dkfS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 26044.152 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 26600.010 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-OLA / ![]() |
#4: Chemical | ChemComp-BMS / |
#5: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.24 % |
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Crystal grow![]() | Temperature: 297 K / Method: vapor diffusion, hanging drop / Details: 23% PEG 10,000 0.1 M Hepes, pH 7.25 |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Dec 5, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.76→19.47 Å / Biso Wilson estimate: 47.78 Å2 |
Reflection shell | Resolution: 2.76→2.86 Å |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1dkf Resolution: 2.76→19.82 Å / SU ML: 0.2487 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.2324 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.76→19.82 Å
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Refine LS restraints |
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LS refinement shell |
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