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Yorodumi- PDB-1rdt: Crystal Structure of a new rexinoid bound to the RXRalpha ligand ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rdt | ||||||
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Title | Crystal Structure of a new rexinoid bound to the RXRalpha ligand binding doamin in the RXRalpha/PPARgamma heterodimer | ||||||
Components |
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Keywords | HORMONE/GROWTH FACTOR / Hormone / receptor / polymorphism / HORMONE-GROWTH FACTOR COMPLEX | ||||||
Function / homology | Function and homology information DNA binding domain binding / 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 / peptide lactyltransferase (CoA-dependent) activity / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / LBD domain binding ...DNA binding domain binding / 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 / peptide lactyltransferase (CoA-dependent) activity / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / LBD domain binding / NFE2L2 regulating ER-stress associated genes / Carnitine metabolism / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / retinoic acid binding / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / labyrinthine layer morphogenesis / MRF binding / regulation of thyroid hormone receptor signaling pathway / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / positive regulation of female receptivity / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of NFE2L2 gene expression / negative regulation of transcription by RNA polymerase I / NOTCH3 Intracellular Domain Regulates Transcription / NFE2L2 regulating anti-oxidant/detoxification enzymes / Signaling by Retinoic Acid / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / nuclear steroid receptor activity / positive regulation of cholesterol efflux / embryonic digit morphogenesis / hypothalamus development / male mating behavior / retinoic acid receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / homeostatic process / protein acetylation / Notch-HLH transcription pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / acetyltransferase activity / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to Thyroglobulin triiodothyronine / histone acetyltransferase complex / estrous cycle / positive regulation of double-strand break repair via homologous recombination / Synthesis of bile acids and bile salts / Transcriptional and post-translational regulation of MITF-M expression and activity / Complex I biogenesis / Attenuation phase / positive regulation of adipose tissue development / cellular response to nutrient levels / hormone-mediated signaling pathway / peroxisome proliferator activated receptor signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Respiratory electron transport / positive regulation of bone mineralization / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / regulation of cellular response to insulin stimulus / canonical NF-kappaB signal transduction / response to retinoic acid / regulation of cellular response to heat / mitochondrial ATP synthesis coupled electron transport / histone acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / mitochondrial respiratory chain complex I assembly / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RORA activates gene expression / transcription coregulator binding / NPAS4 regulates expression of target genes / positive regulation of neuron differentiation / lactation / Regulation of lipid metabolism by PPARalpha / CD209 (DC-SIGN) signaling Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Haffner, C.D. / Lenhard, J.M. / Miller, A.B. / McDougald, D.L. / Dwornik, K. / Ittoop, O.R. / Gampe Jr., R.T. / Xu, H.E. / Blanchard, S. / Montana, V.G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2004 Title: Structure-based design of potent retinoid X receptor alpha agonists. Authors: Haffner, C.D. / Lenhard, J.M. / Miller, A.B. / McDougald, D.L. / Dwornik, K. / Ittoop, O.R. / Gampe Jr., R.T. / Xu, H.E. / Blanchard, S. / Montana, V.G. / Consler, T.G. / Bledsoe, R.K. / Ayscue, A. / Croom, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rdt.cif.gz | 118 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rdt.ent.gz | 87.5 KB | Display | PDB format |
PDBx/mmJSON format | 1rdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rdt_validation.pdf.gz | 543.5 KB | Display | wwPDB validaton report |
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Full document | 1rdt_full_validation.pdf.gz | 556.4 KB | Display | |
Data in XML | 1rdt_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 1rdt_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/1rdt ftp://data.pdbj.org/pub/pdb/validation_reports/rd/1rdt | HTTPS FTP |
-Related structure data
Related structure data | 1fm9S 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
-Protein , 2 types, 2 molecules AD
#1: Protein | Mass: 27114.465 Da / Num. of mol.: 1 / Fragment: ligand binding doamin Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Plasmid: pACYC184 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19793 |
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#3: Protein | Mass: 32557.824 Da / Num. of mol.: 1 / Fragment: ligand binding doamin Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37231 |
-Protein/peptide , 2 types, 2 molecules BE
#2: Protein/peptide | Mass: 2806.163 Da / Num. of mol.: 1 / Fragment: LxxLL peptide / Source method: obtained synthetically / References: UniProt: Q15788*PLUS |
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#4: Protein/peptide | Mass: 2368.647 Da / Num. of mol.: 1 / Fragment: LxxLL peptide / Source method: obtained synthetically / References: UniProt: Q92793*PLUS |
-Non-polymers , 3 types, 207 molecules
#5: Chemical | ChemComp-L79 / ( |
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#6: Chemical | ChemComp-570 / |
#7: 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: 2.21 Å3/Da / Density % sol: 44.43 % |
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Crystal grow | Temperature: 295 K / pH: 7.5 Details: 17% PEG 4K, 200mM NaSCN, 8% ethylene glycol, 8% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 8, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 25137 / % possible obs: 98.6 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 36.9 |
Reflection shell | Highest resolution: 2.3 Å / Rmerge(I) obs: 0.422 / % possible all: 86.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FM9 Resolution: 2.4→20 Å / Rfactor Rfree error: 0.06 / Data cutoff low absF: 330222 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 41.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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