+Open data
-Basic information
Entry | Database: PDB / ID: 1ot7 | ||||||
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Title | Structural Basis for 3-deoxy-CDCA Binding and Activation of FXR | ||||||
Components |
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Keywords | HORMONE/GROWTH FACTOR RECEPTOR / BILE ACID / NUCLEAR RECEPTOR / COACTIVATOR / LIGAND BINDING DOMAIN / FXR / HORMONE-GROWTH FACTOR RECEPTOR COMPLEX | ||||||
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 / regulation of carbohydrate metabolic process / regulation of lipid storage / hepatocyte proliferation ...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 / regulation of carbohydrate metabolic process / regulation of lipid storage / 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 / Nuclear Receptor transcription pathway / negative regulation of very-low-density lipoprotein particle remodeling / negative regulation of interleukin-1 production / leukocyte migration involved in inflammatory response / regulation of insulin secretion involved in cellular response to glucose stimulus / cellular response to organonitrogen compound / toll-like receptor 9 signaling pathway / triglyceride homeostasis / 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 / bile acid binding / bile acid signaling pathway / negative regulation of interleukin-2 production / cellular response to fatty acid / positive regulation of interleukin-17 production / positive regulation of insulin secretion involved in cellular response to glucose stimulus / intracellular glucose homeostasis / negative regulation of interleukin-6 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / fatty acid homeostasis / response to glucose / nuclear retinoid X receptor binding / negative regulation of canonical NF-kappaB signal transduction / positive regulation of insulin receptor signaling pathway / Notch signaling pathway / positive regulation of adipose tissue development / response to nutrient levels / cholesterol homeostasis / liver regeneration / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / euchromatin / response to organic cyclic compound / negative regulation of inflammatory response / response to estrogen / nuclear receptor activity / cellular response to xenobiotic stimulus / glucose homeostasis / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / cellular response to lipopolysaccharide / sequence-specific DNA binding / response to lipopolysaccharide / transcription by RNA polymerase II / cell differentiation / receptor complex / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to bacterium / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / protein-containing complex binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 | 1ot7.cif.gz | 115.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ot7.ent.gz | 89.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ot7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/1ot7 ftp://data.pdbj.org/pub/pdb/validation_reports/ot/1ot7 | 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 subunits(A or B). |
-Components
#1: Protein | Mass: 26752.787 Da / Num. of mol.: 2 / Fragment: ligand binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: NR1H4 / Plasmid: pET-16b / 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: GRIP1 NID3 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans #3: Chemical | ChemComp-CHC / | #4: Chemical | ChemComp-IU5 / | #5: 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: 3.18 Å3/Da / Density % sol: 61 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: PEG 8000, Ethylene glycol, PIPES, Ammonium Sulfate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 282K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: NSLS / Beamline: X4A / Wavelength: 1.067 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 25, 2002 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.067 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 17120 / Num. obs: 16726 / % possible obs: 97.7 % / Observed criterion σ(I): 2.5 / Redundancy: 4.7 % / Biso Wilson estimate: 44.5 Å2 / Rsym value: 0.071 / Net I/σ(I): 14.41 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2 / Num. unique all: 1612 / Rsym value: 0.458 / % possible all: 96.5 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. obs: 12668 / % possible obs: 98.9 % / Num. measured all: 99535 / Rmerge(I) obs: 0.071 |
Reflection shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 99.6 % / Rmerge(I) obs: 0.458 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: RAR LBD Resolution: 2.9→19.96 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 18.1809 Å2 / ksol: 0.244014 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.9 Å2
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Refine analyze | Luzzati coordinate error free: 0.55 Å / Luzzati sigma a free: 0.46 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.03 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 8
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Xplor file |
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Refinement | *PLUS Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.29 / Rfactor Rwork: 0.254 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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