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Yorodumi- PDB-6s4n: LXRbeta ligand binding domain in comlpex with small molecule inhi... -
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-Basic information
Entry | Database: PDB / ID: 6s4n | ||||||
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Title | LXRbeta ligand binding domain in comlpex with small molecule inhibitors | ||||||
Components | Oxysterols receptor LXR-beta | ||||||
Keywords | NUCLEAR PROTEIN / liver X receptor beta / LXRb / LXR beta / Nuclear hormone receptor / receptor ligand binding domain | ||||||
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 / positive regulation of protein metabolic process / VLDLR internalisation and degradation / 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: 1.9 Å | ||||||
Authors | Sandmark, J. / Jansson, A. | ||||||
Citation | Journal: Commun Biol / Year: 2019 Title: Structural analysis identifies an escape route from the adverse lipogenic effects of liver X receptor ligands. Authors: Belorusova, A.Y. / Evertsson, E. / Hovdal, D. / Sandmark, J. / Bratt, E. / Maxvall, I. / Schulman, I.G. / Akerblad, P. / Lindstedt, E.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s4n.cif.gz | 217.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s4n.ent.gz | 173.2 KB | Display | PDB format |
PDBx/mmJSON format | 6s4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s4/6s4n ftp://data.pdbj.org/pub/pdb/validation_reports/s4/6s4n | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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-Components
#1: Protein | Mass: 28271.482 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NR1H2, LXRB, NER, UNR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P55055 #2: Chemical | ChemComp-KUW / #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.44 Å3/Da / Density % sol: 49.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M HEPES pH 7.5 and 18% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 30, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→89.1 Å / Num. obs: 104549 / % possible obs: 92.7 % / Redundancy: 2 % / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.9→2 Å / Num. unique obs: 12776 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→54.718 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.917 / Cross valid method: FREE R-VALUE / ESU R: 0.195 / ESU R Free: 0.164 Details: Hydrogens have been added in their 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.876 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→54.718 Å
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