+Open data
-Basic information
Entry | Database: PDB / ID: 6ssq | ||||||
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Title | Crystal structure of RARbeta LBD in complex with LG 100754 | ||||||
Components |
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Keywords | TRANSCRIPTION / Nuclear receptor / Ligand binding | ||||||
Function / homology | Function and homology information ventricular cardiac muscle cell differentiation / embryonic eye morphogenesis / glandular epithelial cell development / growth plate cartilage development / embryonic digestive tract development / striatum development / neural precursor cell proliferation / labyrinthine layer morphogenesis / negative regulation of chondrocyte differentiation / regulation of thyroid hormone mediated signaling pathway ...ventricular cardiac muscle cell differentiation / embryonic eye morphogenesis / glandular epithelial cell development / growth plate cartilage development / embryonic digestive tract development / striatum development / neural precursor cell proliferation / labyrinthine layer morphogenesis / negative regulation of chondrocyte differentiation / regulation of thyroid hormone mediated signaling pathway / embryonic hindlimb morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / ureteric bud development / regulation of myelination / Signaling by Retinoic Acid / hypothalamus development / male mating behavior / heterocyclic compound binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / estrous cycle / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / retinoic acid receptor signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / response to retinoic acid / negative regulation of stem cell proliferation / histone acetyltransferase activity / 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 / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / neurogenesis / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / response to progesterone / stem cell proliferation / nuclear estrogen receptor binding / nuclear receptor binding / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / multicellular organism growth / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / response to estradiol / HATs acetylate histones / Estrogen-dependent gene expression / transcription regulator complex / cell differentiation / transcription coactivator activity / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / apoptotic process / chromatin binding / chromatin / protein-containing complex binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | le Maire, A. / Teyssier, C. / Germain, P. / Bourguet, W. | ||||||
Citation | Journal: Cells / Year: 2019 Title: Regulation of RXR-RAR Heterodimers by RXR- and RAR-Specific Ligands and Their Combinations. Authors: le Maire, A. / Teyssier, C. / Balaguer, P. / Bourguet, W. / Germain, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ssq.cif.gz | 220.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ssq.ent.gz | 174.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ssq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ss/6ssq ftp://data.pdbj.org/pub/pdb/validation_reports/ss/6ssq | HTTPS FTP |
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-Related structure data
Related structure data | 6stiC 4jyiS 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
-Protein / Protein/peptide , 2 types, 4 molecules ABFG
#1: Protein | Mass: 30197.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RARB, HAP, NR1B2 / Production host: Escherichia coli (E. coli) / References: UniProt: P10826 #2: Protein/peptide | Mass: 1591.880 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NCOA1, BHLHE74, SRC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15788, histone acetyltransferase |
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-Non-polymers , 4 types, 130 molecules
#3: Chemical | #4: Chemical | ChemComp-FLC / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.13 Å3/Da / Density % sol: 42.35 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 200 mM Tri Sodium Citrate pH 5.5, 25 % PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0017 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0017 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→67.24 Å / Num. obs: 24860 / % possible obs: 99.94 % / Redundancy: 11.5 % / CC1/2: 0.713 / Net I/σ(I): 46.49 |
Reflection shell | Resolution: 2.3→2.382 Å / Num. unique obs: 2449 / CC1/2: 0.435 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JYI Resolution: 2.3→67.24 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.3→67.24 Å
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