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Yorodumi- PDB-1fm9: THE 2.1 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE HETERODIMER ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fm9 | ||||||
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Title | THE 2.1 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE HETERODIMER OF THE HUMAN RXRALPHA AND PPARGAMMA LIGAND BINDING DOMAINS RESPECTIVELY BOUND WITH 9-CIS RETINOIC ACID AND GI262570 AND CO-ACTIVATOR PEPTIDES. | ||||||
Components |
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Keywords | TRANSCRIPTION / the heterodimer of the nuclear receptor ligand binding domains of RXRalpha and PPARgamma bound respectively with 9-cis Retinoic Acid and GI262570 and co-activator peptides | ||||||
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 / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / LBD domain binding / Carnitine metabolism ...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 / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / LBD domain binding / Carnitine metabolism / retinoic acid binding / labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / 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 / Signaling by Retinoic Acid / nuclear steroid receptor activity / positive regulation of cholesterol efflux / hypothalamus development / male mating behavior / retinoic acid receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to Thyroglobulin triiodothyronine / estrous cycle / Synthesis of bile acids and bile salts / Complex I biogenesis / positive regulation of adipose tissue development / 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 / response to retinoic acid / 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 / RORA activates gene expression / transcription coregulator binding / positive regulation of neuron differentiation / lactation / Regulation of lipid metabolism by PPARalpha / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / peptide binding / : / mitochondrial electron transport, NADH to ubiquinone / SUMOylation of intracellular receptors / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / mRNA transcription by RNA polymerase II / response to progesterone / nuclear receptor binding / NADH dehydrogenase (ubiquinone) activity / hippocampus development / nuclear estrogen receptor binding / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PPARA activates gene expression / Heme signaling / Nuclear Receptor transcription pathway / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / mitochondrial membrane / aerobic respiration / Cytoprotection by HMOX1 / RNA polymerase II transcription regulator complex / cerebral cortex development / nuclear receptor activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / male gonad development / sequence-specific double-stranded DNA binding / Circadian Clock / response to estradiol / double-stranded DNA binding / HATs acetylate histones / transcription regulator complex / sequence-specific DNA binding / Estrogen-dependent gene expression / transcription coactivator activity / transcription cis-regulatory region binding / receptor complex / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / mitochondrial inner membrane / RNA polymerase II cis-regulatory region sequence-specific DNA binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Gampe Jr., R.T. / Montana, V.G. / Lambert, M.H. / Miller, A.B. / Bledsoe, R.K. / Milburn, M.V. / Kliewer, S.A. / Willson, T.M. / Xu, H.E. | ||||||
Citation | Journal: Mol.Cell / Year: 2000 Title: Asymmetry in the PPARgamma/RXRalpha crystal structure reveals the molecular basis of heterodimerization among nuclear receptors. Authors: Gampe Jr., R.T. / Montana, V.G. / Lambert, M.H. / Miller, A.B. / Bledsoe, R.K. / Milburn, M.V. / Kliewer, S.A. / Willson, T.M. / Xu, H.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fm9.cif.gz | 123 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fm9.ent.gz | 93.2 KB | Display | PDB format |
PDBx/mmJSON format | 1fm9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fm9_validation.pdf.gz | 1020.3 KB | Display | wwPDB validaton report |
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Full document | 1fm9_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1fm9_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 1fm9_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/1fm9 ftp://data.pdbj.org/pub/pdb/validation_reports/fm/1fm9 | HTTPS FTP |
-Related 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: 26667.857 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN - RESIDUES 225 - 462 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / 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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#2: Protein | Mass: 31094.135 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN - RESIDUES 206 - 477 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37231 |
-Protein/peptide , 1 types, 2 molecules BE
#3: Protein/peptide | Mass: 2806.163 Da / Num. of mol.: 2 / Fragment: SRC-1 PEPTIDE / Source method: obtained synthetically Details: Chemically synthesized 25mer portion of human src-1 coactivator peptide References: UniProt: O43793, UniProt: Q15788*PLUS |
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-Non-polymers , 3 types, 133 molecules
#4: Chemical | ChemComp-9CR / ( |
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#5: Chemical | ChemComp-570 / |
#6: Water | ChemComp-HOH / |
-Details
Nonpolymer details | GI262570 is a synthetic antidiabetic agonist for PPARGAMMA |
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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: 2.07 Å3/Da / Density % sol: 40.72 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 17% PEG 4K, 200mM NaSCN, 8% Ethylene Glycol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 35 % | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-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: Dec 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 25483 / % possible obs: 98.8 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 21.2 |
Reflection shell | *PLUS Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Resolution: 2.1→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 149063.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55 Å2 / ksol: 0.382 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 49 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.334 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.308 |