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Yorodumi- PDB-7prv: The glucocorticoid receptor in complex with fluticasone furoate, ... -
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-Basic information
Entry | Database: PDB / ID: 7prv | ||||||
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Title | The glucocorticoid receptor in complex with fluticasone furoate, a PGC1a coactivator fragment and sgk 23bp | ||||||
Components |
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Keywords | SIGNALING PROTEIN / nuclear receptor / ligand-activated transcription factor / multi-domain / complex / agonist | ||||||
Function / homology | Function and homology information positive regulation of mitochondrial DNA metabolic process / positive regulation of muscle tissue development / Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / positive regulation of cellular respiration / positive regulation of fatty acid oxidation / steroid hormone binding / PTK6 Expression / neuroinflammatory response ...positive regulation of mitochondrial DNA metabolic process / positive regulation of muscle tissue development / Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / positive regulation of cellular respiration / positive regulation of fatty acid oxidation / steroid hormone binding / PTK6 Expression / neuroinflammatory response / glucocorticoid metabolic process / : / microglia differentiation / maternal behavior / mammary gland duct morphogenesis / nucleus localization / astrocyte differentiation / : / lncRNA binding / cellular respiration / cellular response to glucocorticoid stimulus / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / motor behavior / temperature homeostasis / regulation of gluconeogenesis / adrenal gland development / cellular response to steroid hormone stimulus / positive regulation of ATP biosynthetic process / response to starvation / intracellular glucose homeostasis / fatty acid oxidation / response to dietary excess / estrogen response element binding / adipose tissue development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / energy homeostasis / intracellular steroid hormone receptor signaling pathway / brown fat cell differentiation / core promoter sequence-specific DNA binding / positive regulation of gluconeogenesis / digestion / cellular response to transforming growth factor beta stimulus / respiratory electron transport chain / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / TBP-class protein binding / steroid binding / cellular response to dexamethasone stimulus / mitochondrion organization / RNA splicing / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / synaptic transmission, glutamatergic / chromosome segregation / gluconeogenesis / transcription initiation at RNA polymerase II promoter / nuclear receptor binding / transcription coregulator activity / negative regulation of smooth muscle cell proliferation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / PML body / spindle / chromatin DNA binding / mRNA processing / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / positive regulation of neuron apoptotic process / Regulation of RUNX2 expression and activity / nuclear receptor activity / positive regulation of DNA-binding transcription factor activity / Circadian Clock / sequence-specific double-stranded DNA binding / cellular response to oxidative stress / positive regulation of cold-induced thermogenesis / gene expression / chromatin organization / DNA-binding transcription activator activity, RNA polymerase II-specific / protein-containing complex assembly / neuron apoptotic process / DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / sequence-specific DNA binding / transcription coactivator activity / protein stabilization / DNA-binding transcription factor activity, RNA polymerase II-specific / mitochondrial matrix / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Postel, S. / Edman, K. / Wissler, L. | ||||||
Funding support | 1items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2023 Title: Quaternary glucocorticoid receptor structure highlights allosteric interdomain communication. Authors: Postel, S. / Wissler, L. / Johansson, C.A. / Gunnarsson, A. / Gordon, E. / Collins, B. / Castaldo, M. / Kohler, C. / Oling, D. / Johansson, P. / Froderberg Roth, L. / Beinsteiner, B. / ...Authors: Postel, S. / Wissler, L. / Johansson, C.A. / Gunnarsson, A. / Gordon, E. / Collins, B. / Castaldo, M. / Kohler, C. / Oling, D. / Johansson, P. / Froderberg Roth, L. / Beinsteiner, B. / Dainty, I. / Delaney, S. / Klaholz, B.P. / Billas, I.M.L. / Edman, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7prv.cif.gz | 337.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7prv.ent.gz | 271.8 KB | Display | PDB format |
PDBx/mmJSON format | 7prv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/7prv ftp://data.pdbj.org/pub/pdb/validation_reports/pr/7prv | HTTPS FTP |
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-Related structure data
Related structure data | 7prwC 7prxC 3g9oS 4p6wS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 7064.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#3: DNA chain | Mass: 7015.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Protein / Protein/peptide , 2 types, 3 molecules ABF
#1: Protein | Mass: 44511.457 Da / Num. of mol.: 2 / Mutation: S404A, N517D, V571M, F602S, C638D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NR3C1, GRL / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04150 #4: Protein/peptide | | Mass: 2261.611 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2 |
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-Non-polymers , 4 types, 39 molecules
#5: Chemical | ChemComp-ZN / #6: Chemical | #7: Chemical | #8: 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: 3.02 Å3/Da / Density % sol: 63.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 8 % PEG3350, 0.3 M 1,6-hexanediol, 0.1 M guanidine hydrochloride, 8 % 2,2,2-trifluoroethanol, 0.1 M Bis Tris Propane pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96545 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96545 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→68.684 Å / Num. obs: 24963 / % possible obs: 93.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.029 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.7→3.005 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.035 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1248 / Rpim(I) all: 0.425 / % possible all: 63.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3g9O, 4P6W Resolution: 2.7→68.68 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.382
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Displacement parameters | Biso mean: 103.55 Å2
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Refine analyze | Luzzati coordinate error obs: 0.4 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→68.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.88 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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