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- PDB-1s0x: Crystal structure of the human RORalpha ligand binding domain in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1s0x | ||||||
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Title | Crystal structure of the human RORalpha ligand binding domain in complex with cholesterol sulfate at 2.2A | ||||||
![]() | Nuclear receptor ROR-alpha | ||||||
![]() | hormone/growth factor receptor / THREE-LAYERED ALPHA HELICAL SANDWICH / NUCLEAR HORMONE RECEPTOR / ORPHAN RECEPTOR / LIGAND BINDING DOMAIN / hormone-growth factor receptor COMPLEX | ||||||
Function / homology | ![]() cGMP metabolic process / cerebellar Purkinje cell differentiation / cerebellar granule cell precursor proliferation / T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / muscle cell differentiation / intracellular receptor signaling pathway / positive regulation of circadian rhythm ...cGMP metabolic process / cerebellar Purkinje cell differentiation / cerebellar granule cell precursor proliferation / T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / muscle cell differentiation / intracellular receptor signaling pathway / positive regulation of circadian rhythm / oxysterol binding / regulation of smoothened signaling pathway / triglyceride homeostasis / regulation of macrophage activation / negative regulation of fat cell differentiation / regulation of glucose metabolic process / positive regulation of vascular endothelial growth factor production / cellular response to interleukin-1 / negative regulation of canonical NF-kappaB signal transduction / nitric oxide biosynthetic process / RORA activates gene expression / xenobiotic metabolic process / transcription corepressor binding / transcription coregulator binding / cholesterol homeostasis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / PPARA activates gene expression / beta-catenin binding / transcription coactivator binding / negative regulation of inflammatory response / Nuclear Receptor transcription pathway / nuclear receptor activity / Circadian Clock / cellular response to tumor necrosis factor / cellular response to hypoxia / angiogenesis / Interleukin-4 and Interleukin-13 signaling / sequence-specific DNA 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 / regulation of DNA-templated transcription / chromatin / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kallen, J. / Schlaeppi, J.M. / Bitsch, F. / Delhon, I. / Fournier, B. | ||||||
![]() | ![]() Title: Crystal structure of the human RORalpha Ligand binding domain in complex with cholesterol sulfate at 2.2 A Authors: Kallen, J. / Schlaeppi, J.M. / Bitsch, F. / Delhon, I. / Fournier, B. #1: ![]() Title: X-ray structure of the hRORalpha LBD at 1.63A: Structural and functional data that cholesterol or a cholesterol derivative is the natural ligand of RORalpha Authors: Kallen, J. / Schlaeppi, J.-M. / Bitsch, F. / Geisse, S. / Geiser, M. / Delhon, I. / Fournier, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.2 KB | Display | ![]() |
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PDB format | ![]() | 52.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 679.8 KB | Display | ![]() |
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Full document | ![]() | 683.4 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 21.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1n83S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | Biological assembly is monomer |
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Components
#1: Protein | Mass: 31514.279 Da / Num. of mol.: 1 / Fragment: ligand binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-C3S / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.39 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 17, 2002 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 16541 / Num. obs: 16541 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.2→2.28 Å / % possible all: 99.4 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 57993 |
Reflection shell | *PLUS % possible obs: 99.4 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1N83 Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.909 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.919 Å2
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Refine analyze | Luzzati coordinate error free: 0.181 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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Software | *PLUS Version: 5 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.219 / Rfactor Rwork: 0.194 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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