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Yorodumi- PDB-1dkf: CRYSTAL STRUCTURE OF A HETERODIMERIC COMPLEX OF RAR AND RXR LIGAN... -
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-Basic information
Entry | Database: PDB / ID: 1dkf | ||||||
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Title | CRYSTAL STRUCTURE OF A HETERODIMERIC COMPLEX OF RAR AND RXR LIGAND-BINDING DOMAINS | ||||||
Components |
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Keywords | HORMONE/GROWTH FACTOR RECEPTOR / HELICAL SANDWICH / HETERODIMER / PROTEIN-LIGAND COMPLEX / Structural Proteomics in Europe / SPINE / Structural Genomics / HORMONE-GROWTH FACTOR RECEPTOR complex | ||||||
Function / homology | Function and homology information Transcriptional regulation of granulopoiesis / Carnitine metabolism / Transcriptional regulation of white adipocyte differentiation / Sertoli cell fate commitment / Signaling by Retinoic Acid / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of binding / SUMOylation of intracellular receptors / trachea cartilage development ...Transcriptional regulation of granulopoiesis / Carnitine metabolism / Transcriptional regulation of white adipocyte differentiation / Sertoli cell fate commitment / Signaling by Retinoic Acid / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of binding / SUMOylation of intracellular receptors / trachea cartilage development / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / Nuclear Receptor transcription pathway / ventricular cardiac muscle cell differentiation / visceral serous pericardium development / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / mesenchyme development / positive regulation of translational initiation by iron / Endogenous sterols / embryonic camera-type eye development / chondroblast differentiation / glandular epithelial cell development / maternal placenta development / negative regulation of granulocyte differentiation / protein kinase B binding / growth plate cartilage development / positive regulation of T-helper 2 cell differentiation / prostate gland development / negative regulation of cartilage development / Regulation of lipid metabolism by PPARalpha / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / retinoic acid-responsive element binding / regulation of hematopoietic progenitor cell differentiation / Cytoprotection by HMOX1 / positive regulation of thyroid hormone receptor signaling pathway / positive regulation of interleukin-13 production / angiogenesis involved in coronary vascular morphogenesis / positive regulation of interleukin-5 production / cardiac muscle cell differentiation / nuclear retinoic acid receptor binding / alpha-actinin binding / camera-type eye development / retinoic acid binding / response to vitamin A / positive regulation of vitamin D receptor signaling pathway / apoptotic cell clearance / limb development / nuclear thyroid hormone receptor binding / cardiac muscle cell proliferation / ventricular cardiac muscle tissue morphogenesis / ureteric bud development / regulation of myelination / protein kinase A binding / Signaling by Retinoic Acid / DNA-binding transcription repressor activity / nuclear steroid receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / regulation of branching involved in prostate gland morphogenesis / retinoic acid receptor signaling pathway / heterocyclic compound binding / positive regulation of interleukin-4 production / face development / germ cell development / negative regulation of tumor necrosis factor production / negative regulation of type II interferon production / cellular response to estrogen stimulus / hormone-mediated signaling pathway / positive regulation of bone mineralization / positive regulation of cell cycle / heart morphogenesis / response to retinoic acid / cellular response to retinoic acid / response to glucocorticoid / negative regulation of miRNA transcription / positive regulation of neuron differentiation / embryo implantation / mRNA regulatory element binding translation repressor activity / liver development / SUMOylation of intracellular receptors / response to cytokine / neural tube closure / mRNA transcription by RNA polymerase II / placenta development / female pregnancy / hippocampus development / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Nuclear Receptor transcription pathway / regulation of synaptic plasticity / multicellular organism growth / chromatin DNA binding / RNA polymerase II transcription regulator complex / transcription coactivator binding / nuclear receptor activity / mRNA 5'-UTR binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone deacetylase binding / sequence-specific double-stranded DNA binding / actin cytoskeleton Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Bourguet, W. / Vivat, V. / Wurtz, J.M. / Chambon, P. / Gronemeyer, H. / Moras, D. / Structural Proteomics in Europe (SPINE) | ||||||
Citation | Journal: Mol.Cell / Year: 2000 Title: Crystal structure of a heterodimeric complex of RAR and RXR ligand-binding domains. Authors: Bourguet, W. / Vivat, V. / Wurtz, J.M. / Chambon, P. / Gronemeyer, H. / Moras, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dkf.cif.gz | 106.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dkf.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 1dkf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dkf_validation.pdf.gz | 905.1 KB | Display | wwPDB validaton report |
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Full document | 1dkf_full_validation.pdf.gz | 924.8 KB | Display | |
Data in XML | 1dkf_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 1dkf_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/1dkf ftp://data.pdbj.org/pub/pdb/validation_reports/dk/1dkf | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25968.055 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: P28700 |
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#2: Protein | Mass: 26600.010 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 (E. coli) / References: UniProt: P10276 |
#3: Chemical | ChemComp-OLA / |
#4: Chemical | ChemComp-BMS / |
#5: 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: 3.88 Å3/Da / Density % sol: 68.27 % | |||||||||||||||
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Crystal grow | pH: 7.25 / Details: PEG 10000, pH 7.25 | |||||||||||||||
Crystal grow | *PLUS Temperature: 24 ℃ / Method: unknown | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.918 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 5, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 29168 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 44.3 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.204 / % possible all: 98.4 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 44.3 Å2 |
Reflection shell | *PLUS % possible obs: 98.4 % / Mean I/σ(I) obs: 3.5 |
-Processing
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Refinement | Resolution: 2.5→20 Å / σ(F): 3
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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