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Yorodumi- PDB-6w9k: Structure of the Ancestral Glucocorticoid Receptor 2 ligand bindi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w9k | |||||||||
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Title | Structure of the Ancestral Glucocorticoid Receptor 2 ligand binding domain in complex with Prednisolone and PGC1a coregulator fragment | |||||||||
Components |
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Keywords | HORMONE / Glucocorticoid Receptor / anti-inflammation drug | |||||||||
Function / homology | Function and homology information Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / lncRNA binding / cellular respiration / temperature homeostasis / response to starvation / intracellular glucose homeostasis / fatty acid oxidation ...Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / lncRNA binding / cellular respiration / temperature homeostasis / response to starvation / intracellular glucose homeostasis / fatty acid oxidation / response to dietary excess / adipose tissue development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / brown fat cell differentiation / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / energy homeostasis / positive regulation of gluconeogenesis / digestion / respiratory electron transport chain / RNA splicing / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / mitochondrion organization / gluconeogenesis / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / positive regulation of DNA-binding transcription factor activity / negative regulation of smooth muscle cell proliferation / transcription coregulator activity / circadian regulation of gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / PML body / chromatin DNA binding / Transcriptional regulation of white adipocyte differentiation / mRNA processing / Regulation of RUNX2 expression and activity / positive regulation of cold-induced thermogenesis / Circadian Clock / cellular response to oxidative stress / protein-containing complex assembly / DNA-binding transcription factor binding / neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / sequence-specific DNA binding / transcription coactivator activity / protein stabilization / ubiquitin protein ligase binding / regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | synthetic construct (others) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Liu, X. / Ortlund, E.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Disruption of a key ligand-H-bond network drives dissociative properties in vamorolone for Duchenne muscular dystrophy treatment. Authors: Liu, X. / Wang, Y. / Gutierrez, J.S. / Damsker, J.M. / Nagaraju, K. / Hoffman, E.P. / Ortlund, E.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w9k.cif.gz | 154 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w9k.ent.gz | 99.9 KB | Display | PDB format |
PDBx/mmJSON format | 6w9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w9k_validation.pdf.gz | 781.7 KB | Display | wwPDB validaton report |
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Full document | 6w9k_full_validation.pdf.gz | 785.7 KB | Display | |
Data in XML | 6w9k_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 6w9k_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/6w9k ftp://data.pdbj.org/pub/pdb/validation_reports/w9/6w9k | HTTPS FTP |
-Related structure data
Related structure data | 6w9lC 6w9mC 3gn8S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28702.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X8XLE9 |
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#2: Protein/peptide | Mass: 1097.434 Da / Num. of mol.: 1 / Fragment: amino acids 142-151 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2 |
#3: Chemical | ChemComp-TUA / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.24 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M ammonium acetate, 3.0 M sodium formate, and 0.1 M HEPES 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→39.25 Å / Num. obs: 48001 / % possible obs: 98.7 % / Redundancy: 12 % / Biso Wilson estimate: 29.1 Å2 / CC1/2: 0.952 / CC star: 0.988 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.6→1.66 Å / Num. unique obs: 4531 / CC1/2: 0.765 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GN8 Resolution: 1.6→39.25 Å / SU ML: 0.1752 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.6239
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→39.25 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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