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- PDB-7yfk: The structure of human pregnane X receptor in complex with an SRC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yfk | |||||||||
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Title | The structure of human pregnane X receptor in complex with an SRC-1 coactivator peptide and a limonoid compound, nomilin | |||||||||
![]() | Nuclear receptor subfamily 1 group I member 2,Nuclear receptor coactivator 1 | |||||||||
![]() | TRANSCRIPTION / Complex / Activator / Drug Binding / Nuclear Receptor | |||||||||
Function / homology | ![]() xenobiotic transport / labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / intermediate filament cytoskeleton / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / steroid metabolic process ...xenobiotic transport / labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / intermediate filament cytoskeleton / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / steroid metabolic process / cellular response to Thyroglobulin triiodothyronine / estrous cycle / Synthesis of bile acids and bile salts / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / xenobiotic catabolic process / nuclear retinoid X receptor binding / response to retinoic acid / 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 / xenobiotic metabolic process / 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 / hippocampus development / nuclear estrogen receptor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / SUMOylation of intracellular receptors / 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 / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / male gonad development / sequence-specific double-stranded DNA binding / Circadian Clock / response to estradiol / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / transcription coactivator activity / cell differentiation / nuclear body / 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 / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / 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 / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Xia, Y. / Yao, D. / Huang, C. / Cao, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Pregnane X receptor agonist nomilin extends lifespan and healthspan in preclinical models through detoxification functions. Authors: Fan, S. / Yan, Y. / Xia, Y. / Zhou, Z. / Luo, L. / Zhu, M. / Han, Y. / Yao, D. / Zhang, L. / Fang, M. / Peng, L. / Yu, J. / Liu, Y. / Gao, X. / Guan, H. / Li, H. / Wang, C. / Wu, X. / Zhu, H. ...Authors: Fan, S. / Yan, Y. / Xia, Y. / Zhou, Z. / Luo, L. / Zhu, M. / Han, Y. / Yao, D. / Zhang, L. / Fang, M. / Peng, L. / Yu, J. / Liu, Y. / Gao, X. / Guan, H. / Li, H. / Wang, C. / Wu, X. / Zhu, H. / Cao, Y. / Huang, C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 258 KB | Display | ![]() |
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PDB format | ![]() | 207.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 35.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5x0rS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38557.348 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: 2-306; pregnane X receptor, 307-321:linker, 313-337:SRC-1, 338-340: tag,2-306; pregnane X receptor, 307-321:linker, 313-337:SRC-1, 338-340: tag Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O75469, UniProt: Q15788, histone acetyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.38 % |
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Crystal grow | Temperature: 277.15 K / Method: evaporation / pH: 8 Details: 10% (v/v) 2-propanol, 100 mM Imidazole/ Hydrochloric acid, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→37.3 Å / Num. obs: 48171 / % possible obs: 99 % / Redundancy: 6.6 % / Biso Wilson estimate: 41.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05394 / Net I/σ(I): 19.68 |
Reflection shell | Resolution: 2.1→2.18 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4750 / CC1/2: 0.809 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5X0R Resolution: 2.1→37.3 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 2.1→37.3 Å
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