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Yorodumi- PDB-2zxz: Crystal structure of the human RXR alpha ligand binding domain bo... -
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-Basic information
Entry | Database: PDB / ID: 2zxz | ||||||
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Title | Crystal structure of the human RXR alpha ligand binding domain bound to a synthetic agonist compound and a coactivator peptide | ||||||
Components |
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Keywords | TRANSCRIPTION / transcription regulation / nuclear receptor / Structural Genomics / Structural Genomics Consortium for Research on Gene Expression / SGCGES | ||||||
Function / homology | Function and homology information positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway ...positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / DNA binding domain binding / nuclear steroid receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / retinoic acid receptor signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of bone mineralization / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / response to retinoic acid / Recycling of bile acids and salts / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / transcription coregulator binding / response to progesterone / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / peptide binding / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / HATs acetylate histones / double-stranded DNA binding / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / cell differentiation / receptor complex / protein dimerization activity / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å | ||||||
Authors | Sato, Y. / Antony, P. / Rochel, N. / Moras, D. / Structural Genomics Consortium for Research on Gene Expression (SGCGES) | ||||||
Citation | Journal: Chemmedchem / Year: 2009 Title: Silicon analogues of the RXR-selective retinoid agonist SR11237 (BMS649): chemistry and biology Authors: Lippert, W.P. / Burschka, C. / Gotz, K. / Kaupp, M. / Ivanova, D. / Gaudon, C. / Sato, Y. / Antony, P. / Rochel, N. / Moras, D. / Gronemeyer, H. / Tacke, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zxz.cif.gz | 59.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zxz.ent.gz | 42.3 KB | Display | PDB format |
PDBx/mmJSON format | 2zxz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/2zxz ftp://data.pdbj.org/pub/pdb/validation_reports/zx/2zxz | HTTPS FTP |
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-Related structure data
Related structure data | 2zy0C 1mznS 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: 26856.039 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19793 |
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#2: Protein/peptide | Mass: 1579.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: Q15596 |
#3: Chemical | ChemComp-P26 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.27 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10mM Tris-HCl, 250mM NaCl, 5mM DTT, 50mM calcium acetate, 18% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2007 |
Radiation | Monochromator: Si(311) or Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 5032 / Num. obs: 5032 / % possible obs: 99.9 % / Redundancy: 12.3 % / Biso Wilson estimate: 57.611 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Χ2: 1.619 / Net I/σ(I): 33.776 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.333 / Num. unique all: 481 / Χ2: 1.014 / % possible all: 100 |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 1MZN Resolution: 3→10 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.87 / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.529 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.75 Å2 / Biso mean: 41.876 Å2 / Biso min: 13.7 Å2
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Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.071 Å / Total num. of bins used: 20
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