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Yorodumi- PDB-4rak: Crystal structure of nuclear receptor subfamily 1, group h, membe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rak | ||||||
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Title | Crystal structure of nuclear receptor subfamily 1, group h, member 2 (lxrb) complexed with partial agonist | ||||||
Components | Oxysterols receptor LXR-beta | ||||||
Keywords | TRANSCRIPTION/AGONIST / NHR / NR1H2 / LXR-B / LXRB / UNR / NER-I / RIP15 / NER / Ligand Binding Domain / Nuclear Hormone Receptor / RXR / TRANSCRIPTION-AGONIST complex | ||||||
Function / homology | Function and homology information positive regulation of secretion of lysosomal enzymes / positive regulation of high-density lipoprotein particle assembly / positive regulation of pancreatic juice secretion / phosphatidylcholine acyl-chain remodeling / positive regulation of cholesterol transport / negative regulation of response to endoplasmic reticulum stress / negative regulation of pinocytosis / positive regulation of lipoprotein lipase activity / apolipoprotein A-I receptor binding / positive regulation of triglyceride biosynthetic process ...positive regulation of secretion of lysosomal enzymes / positive regulation of high-density lipoprotein particle assembly / positive regulation of pancreatic juice secretion / phosphatidylcholine acyl-chain remodeling / positive regulation of cholesterol transport / negative regulation of response to endoplasmic reticulum stress / negative regulation of pinocytosis / positive regulation of lipoprotein lipase activity / apolipoprotein A-I receptor binding / positive regulation of triglyceride biosynthetic process / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of lipid storage / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / positive regulation of fatty acid biosynthetic process / negative regulation of lipid transport / negative regulation of cold-induced thermogenesis / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / negative regulation of macrophage derived foam cell differentiation / positive regulation of cholesterol efflux / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / VLDLR internalisation and degradation / positive regulation of protein metabolic process / hormone-mediated signaling pathway / cholesterol homeostasis / negative regulation of proteolysis / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / PPARA activates gene expression / chromatin DNA binding / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin / 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 / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Nanao, M. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2015 Title: Liver X Receptor (LXR) partial agonists: Biaryl pyrazoles and imidazoles displaying a preference for LXR beta. Authors: Kick, E. / Martin, R. / Xie, Y. / Flatt, B. / Schweiger, E. / Wang, T.L. / Busch, B. / Nyman, M. / Gu, X.H. / Yan, G. / Wagner, B. / Nanao, M. / Nguyen, L. / Stout, T. / Plonowski, A. / ...Authors: Kick, E. / Martin, R. / Xie, Y. / Flatt, B. / Schweiger, E. / Wang, T.L. / Busch, B. / Nyman, M. / Gu, X.H. / Yan, G. / Wagner, B. / Nanao, M. / Nguyen, L. / Stout, T. / Plonowski, A. / Schulman, I. / Ostrowski, J. / Kirchgessner, T. / Wexler, R. / Mohan, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rak.cif.gz | 115.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rak.ent.gz | 89 KB | Display | PDB format |
PDBx/mmJSON format | 4rak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/4rak ftp://data.pdbj.org/pub/pdb/validation_reports/ra/4rak | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30542.854 Da / Num. of mol.: 2 / Fragment: UNP residues 213-460 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NR1H2, LXRB, NER, UNR / References: UniProt: P55055 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.35 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å |
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Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 38284 / % possible obs: 87.2 % / Redundancy: 6.4 % |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→53.21 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.595 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.189 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.366 Å2
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Refine analyze | Luzzati coordinate error obs: 0.304 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→53.21 Å
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Refine LS restraints |
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