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Yorodumi- PDB-3mno: Crystal structure of the agonist form of mouse glucocorticoid rec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mno | ||||||
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Title | Crystal structure of the agonist form of mouse glucocorticoid receptor stabilized by (A611V, F608S) mutations at 1.55A | ||||||
Components |
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Keywords | HORMONE RECEPTOR / protein-ligand complex / steroid nuclear receptor / mouse GR / agonist / co-activator | ||||||
Function / homology | Function and homology information Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / SUMOylation of intracellular receptors / Recycling of bile acids and salts / Nuclear Receptor transcription pathway / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts / negative regulation of synaptic plasticity / positive regulation of glucocorticoid receptor signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand ...Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / SUMOylation of intracellular receptors / Recycling of bile acids and salts / Nuclear Receptor transcription pathway / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts / negative regulation of synaptic plasticity / positive regulation of glucocorticoid receptor signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Endogenous sterols / HATs acetylate histones / intracellular glucocorticoid receptor signaling pathway / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / positive regulation of cell growth involved in cardiac muscle cell development / Regulation of lipid metabolism by PPARalpha / hormone binding / steroid hormone binding / Cytoprotection by HMOX1 / glucocorticoid metabolic process / nuclear glucocorticoid receptor binding / neuroinflammatory response / Estrogen-dependent gene expression / microglia differentiation / maternal behavior / mammary gland duct morphogenesis / nucleus localization / nuclear retinoic acid receptor binding / response to arsenic-containing substance / astrocyte differentiation / negative regulation of vascular permeability / positive regulation of glutamate secretion / positive regulation of female receptivity / cellular response to glucocorticoid stimulus / nuclear thyroid hormone receptor binding / motor behavior / positive regulation of dendritic spine development / regulation of gluconeogenesis / adrenal gland development / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / cellular response to steroid hormone stimulus / postsynaptic density, intracellular component / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / estrogen response element binding / DNA polymerase binding / nuclear retinoid X receptor binding / intracellular steroid hormone receptor signaling pathway / core promoter sequence-specific DNA binding / regulation of cellular response to insulin stimulus / cellular response to hormone stimulus / transcription initiation-coupled chromatin remodeling / Hsp70 protein binding / cellular response to transforming growth factor beta stimulus / positive regulation of adipose tissue development / heat shock protein binding / peroxisome proliferator activated receptor signaling pathway / TBP-class protein binding / steroid binding / cellular response to dexamethasone stimulus / nuclear receptor coactivator activity / response to progesterone / synaptic transmission, glutamatergic / nuclear estrogen receptor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / receptor tyrosine kinase binding / spindle / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / circadian rhythm / RNA polymerase II transcription regulator complex / positive regulation of neuron apoptotic process / nuclear receptor activity / sequence-specific double-stranded DNA binding / gene expression / regulation of cell population proliferation / double-stranded DNA binding / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / dendritic spine / transcription coactivator activity / protein dimerization activity / nuclear body / nuclear speck / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / signaling receptor binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Schoch, G.A. / Seitz, T. / Benz, J. / Banner, D. / Stihle, M. / D'Arcy, B. / Thoma, R. / Sterner, R. / Hennig, M. / Ruf, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Enhancing the stability and solubility of the glucocorticoid receptor ligand-binding domain by high-throughput library screening. Authors: Seitz, T. / Thoma, R. / Schoch, G.A. / Stihle, M. / Benz, J. / D'Arcy, B. / Wiget, A. / Ruf, A. / Hennig, M. / Sterner, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mno.cif.gz | 80 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mno.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 3mno.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/3mno ftp://data.pdbj.org/pub/pdb/validation_reports/mn/3mno | HTTPS FTP |
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-Related structure data
Related structure data | 3mneSC 3mnpC 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, 2 molecules AB
#1: Protein | Mass: 30124.143 Da / Num. of mol.: 1 / Fragment: UNP residues 527-783 / Mutation: A611V, F608S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nr3c1, Grl, Grl1 / Production host: Escherichia coli (E. coli) / References: UniProt: P06537 |
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#2: Protein/peptide | Mass: 1593.844 Da / Num. of mol.: 1 / Fragment: TIF2 coactivator motif, residues 740-752 / Source method: obtained synthetically Details: The sequence occurs naturally in Mus musculus (mouse) References: UniProt: Q61026 |
-Non-polymers , 4 types, 370 molecules
#3: Chemical | #4: Chemical | ChemComp-DEX / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.99 Å3/Da / Density % sol: 58.92 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M sodium thiocyanate, 0.1 M Bis-Tris pH 6.5, 0.7 M lithium sulfate, 10 % Glycerol, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Date: Nov 18, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→35.7 Å / Num. all: 53304 / Num. obs: 53304 / % possible obs: 99.7 % / Redundancy: 11.3 % / Biso Wilson estimate: 23.767 Å2 / Rsym value: 0.067 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 7760 / Rsym value: 0.846 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MNE Resolution: 1.55→35.69 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 30.65 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→35.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.64 Å / Total num. of bins used: 9
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