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Yorodumi- PDB-1upw: Crystal structure of the human Liver X receptor beta ligand bindi... -
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-Basic information
Entry | Database: PDB / ID: 1upw | ||||||
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Title | Crystal structure of the human Liver X receptor beta ligand binding domain in complex with a synthetic agonist | ||||||
Components | OXYSTEROLS RECEPTOR LXR-BETA | ||||||
Keywords | RECEPTOR / NUCLEAR HORMONE RECEPTOR / LIGAND BINDING DOMAIN / LIVER X RECEPTOR / TRANSCRIPTION FACTOR | ||||||
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 type II interferon-mediated signaling pathway / negative regulation of lipid transport / negative regulation of cholesterol storage / negative regulation of macrophage derived foam cell differentiation / negative regulation of cold-induced thermogenesis / positive regulation of cholesterol efflux / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear retinoid X receptor binding / hormone-mediated signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of protein metabolic process / VLDLR internalisation and degradation / positive regulation of miRNA transcription / SUMOylation of intracellular receptors / cholesterol homeostasis / mRNA transcription by RNA polymerase II / negative regulation of proteolysis / PPARA activates gene expression / Nuclear Receptor transcription pathway / chromatin DNA binding / 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 / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Hoerer, S. / Schmid, A. / Heckel, A. / Budzinski, R.M. / Nar, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Crystal Structure of the Human Liver X Receptor Beta Ligand-Binding Domain in Complex with a Synthetic Agonist Authors: Hoerer, S. / Schmid, A. / Heckel, A. / Budzinski, R.M. / Nar, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1upw.cif.gz | 61.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1upw.ent.gz | 43.9 KB | Display | PDB format |
PDBx/mmJSON format | 1upw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1upw_validation.pdf.gz | 465.8 KB | Display | wwPDB validaton report |
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Full document | 1upw_full_validation.pdf.gz | 471.8 KB | Display | |
Data in XML | 1upw_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 1upw_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/1upw ftp://data.pdbj.org/pub/pdb/validation_reports/up/1upw | HTTPS FTP |
-Related structure data
Related structure data | 1upvC 1fcyS C: citing same article (ref.) S: Starting model for refinement |
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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: 29416.621 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 209-461 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P55055 |
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#2: Chemical | ChemComp-444 / |
Compound details | FUNCTION: ORPHAN RECEPTOR. BINDS PREFERENTIALLY TO DOUBLE-STRANDED OLIGONUCLEOTIDE DIRECT REPEATS ...FUNCTION: ORPHAN RECEPTOR. BINDS PREFERENTI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.3 % |
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Crystal grow | pH: 7.5 Details: RESERVOIR: 25% MPD, 10% PEG4K, 100 MM HEPES PH 7.5, 10 MM D PROTEIN: 4-8 MG/ML IN 20 MM TRIS PH 8.0, 100 MM NACL, 10 MM |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9166 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 15, 2002 / Details: MIRRORS |
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9166 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→89 Å / Num. obs: 11049 / % possible obs: 89.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 1.7 / % possible all: 92.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FCY Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.833 / SU B: 10.03 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.518 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.18 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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