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Yorodumi- PDB-4e2j: X-Ray Crystal Structure of the Ancestral Glucocorticoid Receptor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4e2j | ||||||
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Title | X-Ray Crystal Structure of the Ancestral Glucocorticoid Receptor 2 ligand binding domain in complex with mometasone furoate and TIF-2 coactivator fragment | ||||||
Components |
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Keywords | HORMONE/HORMONE ACTIVATOR / nuclear receptor ligand binding domain / glucocorticoid receptor / STEROID BINDING PROTEIN / HORMONE-HORMONE ACTIVATOR complex | ||||||
Function / homology | Function and homology information RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / 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 ...RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / 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 / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / response to progesterone / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / Circadian Clock / HATs acetylate histones / Estrogen-dependent gene expression / transcription regulator complex / transcription coactivator activity / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / chromatin binding / chromatin / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | synthetic construct (others) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kohn, J.A. / Deshpande, K. / Ortlund, E.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Deciphering Modern Glucocorticoid Cross-pharmacology Using Ancestral Corticosteroid Receptors. Authors: Kohn, J.A. / Deshpande, K. / 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 | 4e2j.cif.gz | 119.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e2j.ent.gz | 93.4 KB | Display | PDB format |
PDBx/mmJSON format | 4e2j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/4e2j ftp://data.pdbj.org/pub/pdb/validation_reports/e2/4e2j | HTTPS FTP |
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-Related structure data
Related structure data | 3gn8S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCE
#1: Protein | Mass: 28774.445 Da / Num. of mol.: 2 / Fragment: ligand binding domain / Mutation: F71S Source method: isolated from a genetically manipulated source Details: ancestral gene reconstruction / Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) #2: Protein/peptide | Mass: 1464.664 Da / Num. of mol.: 2 / Fragment: nuclear receptor box 3, UNP residues 741-752 / Source method: obtained synthetically / Details: NR box 3 fragment synthesized by RSSynthesis. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596 |
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-Non-polymers , 4 types, 156 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-FMT / | #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: 3.77 Å3/Da / Density % sol: 67.41 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 1.5-3 M ammonium formate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 12, 2009 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 30710 / Num. obs: 30710 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GN8 Resolution: 2.5→45.19 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.153 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 5.3 / ESU R: 0.325 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.186 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→45.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.501→2.566 Å / Total num. of bins used: 20
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