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Yorodumi- PDB-1r0n: Crystal Structure of Heterodimeric Ecdsyone receptor DNA binding ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r0n | ||||||
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Title | Crystal Structure of Heterodimeric Ecdsyone receptor DNA binding complex | ||||||
Components |
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Keywords | Transcription/DNA / Ecdysone receptor / nuclear receptor / DNA binding domain / Ultraspiracle / RXR / Transcription-DNA COMPLEX | ||||||
Function / homology | Function and homology information repressor ecdysone receptor complex / ecdysis, chitin-based cuticle / larval wandering behavior / regulation of Malpighian tubule diameter / regulation of neuron remodeling / compound eye photoreceptor fate commitment / larval development / ecdysone receptor holocomplex / activator ecdysone receptor complex / dorsal vessel heart proper cell fate commitment ...repressor ecdysone receptor complex / ecdysis, chitin-based cuticle / larval wandering behavior / regulation of Malpighian tubule diameter / regulation of neuron remodeling / compound eye photoreceptor fate commitment / larval development / ecdysone receptor holocomplex / activator ecdysone receptor complex / dorsal vessel heart proper cell fate commitment / hatching / regulation of hemocyte proliferation / Recycling of bile acids and salts / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / histoblast morphogenesis / chitin-based cuticle development / SUMOylation of intracellular receptors / chitin-based embryonic cuticle biosynthetic process / Nuclear Receptor transcription pathway / response to ecdysone / Malpighian tubule morphogenesis / larval central nervous system remodeling / VLDLR internalisation and degradation / head involution / ecdysone binding / germ-band shortening / pupariation / ecdysone receptor-mediated signaling pathway / cardioblast differentiation / regulation of development, heterochronic / positive regulation of neuron remodeling / mushroom body development / metamorphosis / border follicle cell migration / : / sperm individualization / imaginal disc-derived wing morphogenesis / positive regulation of circadian sleep/wake cycle, sleep / polytene chromosome / 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 mediated signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / peripheral nervous system development / Carnitine metabolism / anatomical structure development / ion binding / cardiac muscle tissue development / Regulation of pyruvate dehydrogenase (PDH) complex / retinoic acid binding / regulation of cellular respiration / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / dendrite morphogenesis / Signaling by Retinoic Acid / neuron remodeling / DNA binding domain binding / nuclear steroid receptor activity / oogenesis / phagocytosis, engulfment / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / germ cell development / positive regulation of cholesterol efflux / Synthesis of bile acids and bile salts / long-term memory / epidermis development / 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 / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to retinoic acid / core promoter sequence-specific DNA binding / Recycling of bile acids and salts / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / steroid binding / hormone-mediated signaling pathway / cholesterol homeostasis / response to cocaine / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / transcription corepressor binding / regulation of autophagy / determination of adult lifespan / transcription coregulator binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å | ||||||
Authors | Devarakonda, S. / Harp, J.M. / Kim, Y. / Ozyhar, A. / Rastinejad, F. | ||||||
Citation | Journal: Embo J. / Year: 2003 Title: Structure of the heterodimeric Ecdysone Receptor DNA-binding complex Authors: Devarakonda, S. / Harp, J.M. / Kim, Y. / Ozyhar, A. / Rastinejad, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r0n.cif.gz | 70 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r0n.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 1r0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/1r0n ftp://data.pdbj.org/pub/pdb/validation_reports/r0/1r0n | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is the macromolecular complex in the asymmetric unit and consists of two DNA binding domains (EcR and RXR), bound to an ecdysone response element (IR-1) |
-Components
-DNA chain , 2 types, 2 molecules CD
#1: DNA chain | Mass: 5501.567 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 5492.553 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 2 types, 2 molecules AB
#3: Protein | Mass: 9375.969 Da / Num. of mol.: 1 / Fragment: Retinoid X Receptor DNA binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA / Plasmid: pGEX-4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P19793 |
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#4: Protein | Mass: 12554.819 Da / Num. of mol.: 1 / Fragment: Ecdsyone Receptor DNA binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: ECR / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P34021 |
-Non-polymers , 2 types, 108 molecules
#5: Chemical | ChemComp-ZN / #6: Water | ChemComp-HOH / | |
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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: 2.89 Å3/Da / Density % sol: 57.38 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 282 K / Method: vapor diffusion / pH: 5.6 Details: PEG 3350, Lithium Sulfate, Magnesium Sulfate, DTT, Magnesium Chloride, MES, pH 5.6, VAPOR DIFFUSION, temperature 282K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 8 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Zhao, Q., (2000) J.Mol.Biol., 296, 509. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.2834, 1.2837, 1.2155 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 26, 2002 / Details: Mirrors | ||||||||||||
Radiation | Monochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.6→30 Å / Num. all: 12840 / Num. obs: 12403 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 59.5 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 27.5 | ||||||||||||
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 6.7 / Num. unique all: 110 / Rsym value: 0.224 / % possible all: 86.6 | ||||||||||||
Reflection | *PLUS Highest resolution: 2.6 Å / Num. obs: 11884 / Redundancy: 9.8 % / Rmerge(I) obs: 0.102 | ||||||||||||
Reflection shell | *PLUS % possible obs: 75.4 % / Mean I/σ(I) obs: 5.5 |
-Processing
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Refinement | Method to determine structure: MAD / Resolution: 2.6→14.99 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 683925.45 / Data cutoff high rms absF: 683925.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.3423 Å2 / ksol: 0.28339 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→14.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 15 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.282 / Rfactor Rwork: 0.232 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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