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Yorodumi- PDB-1nq7: Characterization of ligands for the orphan nuclear receptor RORbeta -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nq7 | ||||||
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Title | Characterization of ligands for the orphan nuclear receptor RORbeta | ||||||
Components |
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Keywords | TRANSCRIPTION / LIGAND-BINDING DOMAIN / RETINOIDS / RETINOIC ACID / SYNTHETIC LIGAND / ANTAGONIST | ||||||
Function / homology | Function and homology information amacrine cell differentiation / retinal rod cell development / melatonin receptor activity / retinal rod cell differentiation / retinal cone cell development / eye photoreceptor cell development / Nuclear Receptor transcription pathway / labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose ...amacrine cell differentiation / retinal rod cell development / melatonin receptor activity / retinal rod cell differentiation / retinal cone cell development / eye photoreceptor cell development / Nuclear Receptor transcription pathway / labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / estrous cycle / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / negative regulation of osteoblast differentiation / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to retinoic acid / histone acetyltransferase activity / cellular response to retinoic acid / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / histone acetyltransferase / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / RORA activates gene expression / visual perception / lactation / Regulation of lipid metabolism by PPARalpha / cerebellum development / response to hormone / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / response to progesterone / nuclear estrogen receptor binding / nuclear receptor binding / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Transcriptional regulation of white adipocyte differentiation / circadian rhythm / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / response to estradiol / retina development in camera-type eye / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Stehlin-Gaon, C. / Willmann, D. / Sanglier, S. / Van Dorsselaer, A. / Renaud, J.-P. / Moras, D. / Schuele, R. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: All-trans retinoic acid is a ligand for the orphan nuclear receptor RORbeta Authors: Stehlin-Gaon, C. / Willmann, D. / Zeyer, D. / Sanglier, S. / Van Dorsselaer, A. / Renaud, J.-P. / Moras, D. / Schuele, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nq7.cif.gz | 74 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nq7.ent.gz | 53.5 KB | Display | PDB format |
PDBx/mmJSON format | 1nq7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/1nq7 ftp://data.pdbj.org/pub/pdb/validation_reports/nq/1nq7 | HTTPS FTP |
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-Related structure data
Related structure data | 1n4hC 1k4wS 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
#1: Protein | Mass: 28167.613 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: NR1F2 / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P45446 |
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#2: Protein/peptide | Mass: 1290.556 Da / Num. of mol.: 1 / Fragment: SECOND NR-BOX / Source method: obtained synthetically Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN). References: GenBank: 1906028, UniProt: Q15788*PLUS |
#3: Chemical | ChemComp-ARL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG6000, NACL, TRIS-HCL, CHAPS, DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal grow | *PLUS Method: unknown / Details: Potier, N., (2003) Protein Sci., 12, 725. |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.01 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 18, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.01 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. all: 53047 / Num. obs: 52613 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.061 / Net I/σ(I): 32 |
Reflection shell | Resolution: 1.5→1.55 Å / % possible all: 100 |
Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 20 Å / Num. obs: 53123 / % possible obs: 100 % / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 13 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K4W Resolution: 1.5→19.87 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.2813 Å2 / ksol: 0.304355 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→19.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.22 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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