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Yorodumi- PDB-7aos: crystal structure of the RARalpha/RXRalpha ligand binding domain ... -
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-Basic information
Entry | Database: PDB / ID: 7aos | ||||||
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Title | crystal structure of the RARalpha/RXRalpha ligand binding domain heterodimer in complex with a fragment of SRC1 coactivator | ||||||
Components |
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Keywords | HORMONE / Transcription factor / Nuclear hormone receptor / coactivator / agonist / complex | ||||||
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 / labyrinthine layer morphogenesis / positive regulation of vitamin D receptor signaling pathway / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / apoptotic cell clearance / positive regulation of female receptivity / 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 / hypothalamus development / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / regulation of branching involved in prostate gland morphogenesis / male mating behavior / heterocyclic compound binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / 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 / cellular response to Thyroglobulin triiodothyronine / estrous cycle / Synthesis of bile acids and bile salts / retinoic acid receptor signaling pathway / cellular response to estrogen stimulus / 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 / positive regulation of cell cycle / nuclear retinoid X receptor binding / heart morphogenesis / cellular response to retinoic acid / response to retinoic acid / histone acetyltransferase activity / response to glucocorticoid / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | le Maire, A. / Guee, L. / Bourguet, W. | ||||||
Funding support | Brazil, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2021 Title: Structural Insights into the Interaction of the Intrinsically Disordered Co-activator TIF2 with Retinoic Acid Receptor Heterodimer (RXR/RAR). Authors: Senicourt, L. / le Maire, A. / Allemand, F. / Carvalho, J.E. / Guee, L. / Germain, P. / Schubert, M. / Bernado, P. / Bourguet, W. / Sibille, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7aos.cif.gz | 248.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aos.ent.gz | 166.7 KB | Display | PDB format |
PDBx/mmJSON format | 7aos.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7aos_validation.pdf.gz | 476.9 KB | Display | wwPDB validaton report |
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Full document | 7aos_full_validation.pdf.gz | 484.2 KB | Display | |
Data in XML | 7aos_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 7aos_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/7aos ftp://data.pdbj.org/pub/pdb/validation_reports/ao/7aos | HTTPS FTP |
-Related structure data
Related structure data | 7apoC 7bk4C 1xdkS 3kmrS S: Starting model for refinement C: citing same article (ref.) |
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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
-Retinoic acid receptor ... , 2 types, 2 molecules AB
#1: Protein | Mass: 26579.727 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 (bacteria) / References: UniProt: P28700 |
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#2: Protein | Mass: 29967.590 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 (bacteria) / References: UniProt: P10276 |
-Protein/peptide , 1 types, 2 molecules CD
#3: Protein/peptide | Mass: 3105.568 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase |
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-Non-polymers , 4 types, 16 molecules
#4: Chemical | ChemComp-LG2 / |
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#5: Chemical | ChemComp-GOL / |
#6: Chemical | ChemComp-EQN / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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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: 2.33 Å3/Da / Density % sol: 47.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 24% PEG 3350, 0.2M Na acetate, 0.1M Bis Tris Propane pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→48.43 Å / Num. obs: 19916 / % possible obs: 99.95 % / Redundancy: 2 % / Biso Wilson estimate: 60.09 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.83 |
Reflection shell | Resolution: 2.55→2.641 Å / Num. unique obs: 1960 / CC1/2: 0.651 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1xdk + 3kmr Resolution: 2.55→48.43 Å / SU ML: 0.3712 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8441 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→48.43 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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