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Open data
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Basic information
Entry | Database: PDB / ID: 3g8x | ||||||
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Title | GR DNA binding domain:GilZ 16bp complex-65 | ||||||
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![]() | TRANSCRIPTION/DNA / glucocorticoid / DNA-binding / allostery / lever arm / transcription / hormone / Alternative initiation / Chromatin regulator / Cytoplasm / Lipid-binding / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Receptor / Steroid-binding / Transcription regulation / Ubl conjugation / Zinc / Zinc-finger / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | ![]() muscle atrophy / negative regulation of synaptic plasticity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of glucocorticoid receptor signaling pathway / response to inactivity / 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 / SUMOylation of intracellular receptors ...muscle atrophy / negative regulation of synaptic plasticity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of glucocorticoid receptor signaling pathway / response to inactivity / 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 / SUMOylation of intracellular receptors / response to mercury ion / Nuclear Receptor transcription pathway / hormone binding / steroid hormone binding / nucleus localization / neuroinflammatory response / glucocorticoid metabolic process / microglia differentiation / mammary gland duct morphogenesis / maternal behavior / cellular response to magnesium ion / response to arsenic-containing substance / astrocyte differentiation / negative regulation of vascular permeability / positive regulation of glutamate secretion / cellular response to glucocorticoid stimulus / motor behavior / adrenal gland development / cellular response to steroid hormone stimulus / regulation of gluconeogenesis / response to corticosterone / positive regulation of dendritic spine development / response to dexamethasone / androgen metabolic process / regulation of glucose metabolic process / postsynaptic density, intracellular component / estrogen response element binding / cellular response to dexamethasone stimulus / nuclear receptor-mediated steroid hormone signaling pathway / response to electrical stimulus / core promoter sequence-specific DNA binding / cellular response to transforming growth factor beta stimulus / heat shock protein binding / Hsp70 protein binding / steroid binding / TBP-class protein binding / transcription initiation-coupled chromatin remodeling / lung development / positive regulation of miRNA transcription / response to activity / synaptic transmission, glutamatergic / female pregnancy / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / Hsp90 protein binding / response to calcium ion / response to insulin / circadian rhythm / receptor tyrosine kinase binding / nuclear receptor activity / spindle / positive regulation of neuron apoptotic process / sequence-specific double-stranded DNA binding / double-stranded DNA binding / regulation of cell population proliferation / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / protein-containing complex assembly / sequence-specific DNA binding / transcription coactivator activity / dendritic spine / chromatin remodeling / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin binding / centrosome / glutamatergic synapse / regulation of transcription by RNA polymerase II / chromatin / negative regulation of apoptotic process / regulation of DNA-templated transcription / protein-containing complex binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pufall, M.A. / Yamamoto, K.R. / Meijsing, S.H. | ||||||
![]() | ![]() Title: DNA binding site sequence directs glucocorticoid receptor structure and activity. Authors: Meijsing, S.H. / Pufall, M.A. / So, A.Y. / Bates, D.L. / Chen, L. / Yamamoto, K.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 | ![]() | 114 KB | Display | ![]() |
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PDB format | ![]() | 85.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3fylC ![]() 3g6pC ![]() 3g6qC ![]() 3g6rC ![]() 3g6tC ![]() 3g6uC ![]() 3g8uC ![]() 3g97C ![]() 3g99C ![]() 3g9iC ![]() 3g9jC ![]() 3g9mC ![]() 3g9oC ![]() 3g9pC ![]() 1gluS C: citing same article ( S: Starting model for refinement |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 9962.758 Da / Num. of mol.: 2 / Fragment: UNP residues 440-525 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules DC
#2: DNA chain | Mass: 4873.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligonucleotide from Integrated DNA technologies |
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#3: DNA chain | Mass: 4922.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligonucleotide from Integrated DNA technologies |
-Non-polymers , 3 types, 73 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
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#4: Chemical | ChemComp-ZN / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.45 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50mM Na Cacodylate, pH 7.0, 2.25mM Spermine, 9mM MgCl2, 1.8 CoCl2, 5% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 26, 2007 |
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115869 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→40 Å / Num. obs: 21522 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 41.139 Å2 / Rmerge(I) obs: 0.137 / Rsym value: 0.183 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1604 / Rsym value: 0.659 / % possible all: 71.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1GLU Resolution: 2.05→35.363 Å / SU ML: 2.04 / σ(F): 0.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.89 Å2 / ksol: 0.311 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→35.363 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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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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