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Yorodumi- PDB-1osv: STRUCTURAL BASIS FOR BILE ACID BINDING AND ACTIVATION OF THE NUCL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1osv | ||||||
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Title | STRUCTURAL BASIS FOR BILE ACID BINDING AND ACTIVATION OF THE NUCLEAR RECEPTOR FXR | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / LBD / bile acid / coactivator / nuclear receptor | ||||||
Function / homology | Function and homology information response to norepinephrine / Endogenous sterols / Synthesis of bile acids and bile salts / Recycling of bile acids and salts / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / negative regulation of triglyceride biosynthetic process / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recycling of bile acids and salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol ...response to norepinephrine / Endogenous sterols / Synthesis of bile acids and bile salts / Recycling of bile acids and salts / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / negative regulation of triglyceride biosynthetic process / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recycling of bile acids and salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts / regulation of carbohydrate metabolic process / positive regulation of glucocorticoid receptor signaling pathway / regulation of lipid storage / Endogenous sterols / HATs acetylate histones / hepatocyte proliferation / regulation of bile acid secretion / regulation of urea metabolic process / intracellular bile acid receptor signaling pathway / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of glutamate metabolic process / positive regulation of ammonia assimilation cycle / negative regulation of collagen biosynthetic process / bile acid receptor activity / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid / SUMOylation of intracellular receptors / Regulation of lipid metabolism by PPARalpha / Nuclear Receptor transcription pathway / negative regulation of very-low-density lipoprotein particle remodeling / negative regulation of interleukin-1 production / Cytoprotection by HMOX1 / leukocyte migration involved in inflammatory response / nuclear glucocorticoid receptor binding / Estrogen-dependent gene expression / regulation of insulin secretion involved in cellular response to glucose stimulus / cellular response to organonitrogen compound / toll-like receptor 9 signaling pathway / triglyceride homeostasis / nuclear retinoic acid receptor binding / negative regulation of monocyte chemotactic protein-1 production / intracellular receptor signaling pathway / bile acid metabolic process / digestive tract development / bile acid and bile salt transport / response to cholesterol / cell-cell junction assembly / positive regulation of female receptivity / bile acid binding / bile acid signaling pathway / nuclear thyroid hormone receptor binding / negative regulation of interleukin-2 production / cellular response to fatty acid / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / positive regulation of interleukin-17 production / positive regulation of insulin secretion involved in cellular response to glucose stimulus / intracellular glucose homeostasis / locomotor rhythm / negative regulation of interleukin-6 production / aryl hydrocarbon receptor binding / negative regulation of type II interferon production / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / negative regulation of tumor necrosis factor production / regulation of glucose metabolic process / negative regulation of tumor necrosis factor-mediated signaling pathway / fatty acid homeostasis / response to glucose / DNA polymerase binding / nuclear retinoid X receptor binding / negative regulation of canonical NF-kappaB signal transduction / positive regulation of insulin receptor signaling pathway / regulation of cellular response to insulin stimulus / Notch signaling pathway / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / response to nutrient levels / cholesterol homeostasis / nuclear receptor coactivator activity / response to progesterone / liver regeneration / nuclear estrogen receptor binding / transcription coregulator binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / circadian regulation of gene expression / euchromatin / mRNA transcription by RNA polymerase II / response to organic cyclic compound / negative regulation of inflammatory response / circadian rhythm / response to estrogen / RNA polymerase II transcription regulator complex / nuclear receptor activity Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Mi, L.Z. / Devarakonda, S. / Harp, J.M. / Han, Q. / Pellicciari, R. / Willson, T.M. / Khorasanizadeh, S. / Rastinejad, F. | ||||||
Citation | Journal: Mol.Cell / Year: 2003 Title: Structural Basis for Bile Acid Binding and Activation of the Nuclear Receptor FXR Authors: Mi, L.Z. / Devarakonda, S. / Harp, J.M. / Han, Q. / Pellicciari, R. / Willson, T.M. / Khorasanizadeh, S. / Rastinejad, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1osv.cif.gz | 116.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1osv.ent.gz | 91.5 KB | Display | PDB format |
PDBx/mmJSON format | 1osv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/1osv ftp://data.pdbj.org/pub/pdb/validation_reports/os/1osv | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is one of the two subunits in the asymmetric unit - A or B |
-Components
#1: Protein | Mass: 26850.891 Da / Num. of mol.: 2 / Fragment: ligand binding domain (FXR-LBD) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q62735 #2: Protein/peptide | Mass: 1464.664 Da / Num. of mol.: 3 / Fragment: Residues (741-752) / Source method: obtained synthetically Details: The coactivator peptide was synthesized. The sequence of the GRIP is naturally found in Rattus Norvegicus (Norway Rat). References: UniProt: Q61026 #3: Chemical | #4: 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: 3.12 Å3/Da / Density % sol: 60.31 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: PEG 8000,Ethylene Glycol, PIPES , pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 283K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / 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: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0332 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2002 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→24.3 Å / Num. all: 26840 / Num. obs: 24908 / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4 % / Biso Wilson estimate: 44.2 Å2 / Rsym value: 0.044 / Net I/σ(I): 19.61 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.04 / Rsym value: 0.282 / % possible all: 77.2 |
Reflection | *PLUS Lowest resolution: 24.3 Å / Num. obs: 24427 / % possible obs: 92.8 % / Num. measured all: 99829 / Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS % possible obs: 77.2 % / Rmerge(I) obs: 0.282 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.88 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1628529.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.8465 Å2 / ksol: 0.320304 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Lowest resolution: 24.3 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.281 / Rfactor Rwork: 0.251 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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