[English] 日本語
Yorodumi- PDB-7qaa: Crystal structure of RARalpha/RXRalpha ligand binding domain hete... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qaa | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of RARalpha/RXRalpha ligand binding domain heterodimer in complex with BMS614 and oleic acid | ||||||
Components |
| ||||||
Keywords | GENE REGULATION / Nuclear receptor | ||||||
Function / homology | Function and homology information Transcriptional regulation of granulopoiesis / Carnitine metabolism / Transcriptional regulation of white adipocyte differentiation / Regulation of pyruvate dehydrogenase (PDH) complex / 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 ...Transcriptional regulation of granulopoiesis / Carnitine metabolism / Transcriptional regulation of white adipocyte differentiation / Regulation of pyruvate dehydrogenase (PDH) complex / 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 / cellular response to corticotropin-releasing hormone stimulus / growth plate cartilage development / positive regulation of T-helper 2 cell differentiation / prostate gland development / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / negative regulation of cartilage development / Regulation of lipid metabolism by PPARalpha / 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 / nuclear glucocorticoid receptor binding / cardiac muscle cell differentiation / nuclear retinoic acid receptor 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 / ventricular cardiac muscle tissue morphogenesis / cardiac muscle cell proliferation / regulation of myelination / protein kinase A binding / ureteric bud development / 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 / heterocyclic compound binding / positive regulation of interleukin-4 production / face development / alpha-actinin binding / germ cell development / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / retinoic acid receptor signaling pathway / cellular response to estrogen stimulus / positive regulation of bone mineralization / positive regulation of cell cycle / heart morphogenesis / cellular response to retinoic acid / response to retinoic acid / response to glucocorticoid / positive regulation of neuron differentiation / embryo implantation / hormone-mediated signaling pathway / mRNA regulatory element binding translation repressor activity / negative regulation of miRNA transcription / liver development / response to cytokine / neural tube closure / female pregnancy / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / regulation of synaptic plasticity / placenta development / multicellular organism growth / chromatin DNA binding / mRNA 5'-UTR binding / transcription coactivator binding / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Nuclear Receptor transcription pathway / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å | ||||||
Authors | le Maire, A. / Vivat, V. / Guee, L. / Blanc, P. / Malosse, C. / Chamot-Rooke, J. / Germain, P. / Bourguet, w. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: J.Mol.Endocrinol. / Year: 2022 Title: Design and in vitro characterization of RXR variants as tools to investigate the biological role of endogenous rexinoids. Authors: le Maire, A. / Rey, M. / Vivat, V. / Guee, L. / Blanc, P. / Malosse, C. / Chamot-Rooke, J. / Germain, P. / Bourguet, W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7qaa.cif.gz | 129.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7qaa.ent.gz | 79.7 KB | Display | PDB format |
PDBx/mmJSON format | 7qaa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qaa_validation.pdf.gz | 977.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7qaa_full_validation.pdf.gz | 984.5 KB | Display | |
Data in XML | 7qaa_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | 7qaa_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/7qaa ftp://data.pdbj.org/pub/pdb/validation_reports/qa/7qaa | HTTPS FTP |
-Related structure data
Related structure data | 7pdqC 7pdtC 1dkfS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26044.152 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rxra, Nr2b1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P28700 |
---|---|
#2: Protein | Mass: 26600.010 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RARA, NR1B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10276 |
#3: Chemical | ChemComp-OLA / |
#4: Chemical | ChemComp-BMS / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.24 % |
---|---|
Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / Details: 23% PEG 10,000 0.1 M Hepes, pH 7.25 |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.918 Å |
Detector | Type: MAR CCD 130 mm / 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: 2.76→19.47 Å / Biso Wilson estimate: 47.78 Å2 |
Reflection shell | Resolution: 2.76→2.86 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1dkf Resolution: 2.76→19.82 Å / SU ML: 0.2487 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.2324 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.76→19.82 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|