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- PDB-3mne: Crystal structure of the agonist form of mouse glucocorticoid rec... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mne | ||||||
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Title | Crystal structure of the agonist form of mouse glucocorticoid receptor stabilized by F608S mutation at 1.96A | ||||||
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![]() | HORMONE RECEPTOR / protein-ligand complex / steroid nuclear receptor / mouse / agonist / co-activator | ||||||
Function / homology | ![]() Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / SUMOylation of intracellular receptors / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / Nuclear Receptor transcription pathway / negative regulation of synaptic plasticity / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / 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 / Synthesis of bile acids and bile salts / Nuclear Receptor transcription pathway / negative regulation of synaptic plasticity / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / 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 / nuclear receptor-mediated glucocorticoid signaling pathway / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / positive regulation of cell growth involved in cardiac muscle cell development / steroid hormone binding / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / neuroinflammatory response / glucocorticoid metabolic process / hormone binding / Estrogen-dependent gene expression / nuclear glucocorticoid receptor binding / microglia differentiation / mammary gland duct morphogenesis / maternal behavior / 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 / motor behavior / nuclear thyroid hormone receptor binding / regulation of gluconeogenesis / adrenal gland development / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / positive regulation of dendritic spine development / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / postsynaptic density, intracellular component / estrogen response element binding / DNA polymerase binding / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone 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 / cellular response to transforming growth factor beta stimulus / heat shock protein binding / Hsp70 protein binding / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / TBP-class protein binding / steroid binding / cellular response to dexamethasone stimulus / nuclear receptor coactivator activity / synaptic transmission, glutamatergic / response to progesterone / nuclear estrogen receptor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / Hsp90 protein binding / mRNA transcription by RNA polymerase II / receptor tyrosine kinase binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / spindle / circadian rhythm / RNA polymerase II transcription regulator complex / nuclear receptor activity / positive regulation of neuron apoptotic process / regulation of cell population proliferation / gene expression / regulation of gene expression / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / dendritic spine / transcription coactivator activity / nuclear body / protein dimerization activity / 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 / negative regulation of DNA-templated transcription / centrosome / glutamatergic synapse / chromatin binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schoch, G.A. / Seitz, T. / Benz, J. / Banner, D. / Stihle, M. / D'Arcy, B. / Thoma, R. / Sterner, R. / Hennig, M. / Ruf, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.8 KB | Display | ![]() |
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PDB format | ![]() | 56.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 812 KB | Display | ![]() |
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Full document | ![]() | 822.5 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mnoC ![]() 3mnpC ![]() 1m2zS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 30096.092 Da / Num. of mol.: 1 / Fragment: UNP residues 527-783 / Mutation: F608S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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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 | ||||
#3: Chemical | #4: Chemical | ChemComp-DEX / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.67 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7 Details: 0.5 M ammonium sulfate, 0.9 M sodium tartrate, 0.1 M PIPES pH 7.0, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Jul 7, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→12.9 Å / Num. all: 26835 / Num. obs: 26835 / % possible obs: 99.7 % / Redundancy: 11.22 % / Biso Wilson estimate: 26.87 Å2 / Rsym value: 0.051 / Net I/σ(I): 15.72 |
Reflection shell | Resolution: 1.96→2.06 Å / Redundancy: 9.18 % / Mean I/σ(I) obs: 2.41 / Num. unique all: 3555 / Rsym value: 0.4566 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1M2Z Resolution: 1.96→12.98 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 33.3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.1776 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→12.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.08 Å / Total num. of bins used: 9
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