+Open data
-Basic information
Entry | Database: PDB / ID: 3g6r | ||||||
---|---|---|---|---|---|---|---|
Title | GR DNA binding domain:FKBP5 complex-52, 18bp | ||||||
Components |
| ||||||
Keywords | 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 | Function and homology information 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 / 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 / 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 / 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 / SUMOylation of intracellular receptors / response to mercury ion / hormone binding / Nuclear Receptor transcription pathway / steroid hormone binding / glucocorticoid metabolic process / neuroinflammatory response / microglia differentiation / maternal behavior / mammary gland duct morphogenesis / nucleus localization / 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 / positive regulation of dendritic spine development / regulation of gluconeogenesis / adrenal gland development / cellular response to steroid hormone stimulus / response to corticosterone / response to dexamethasone / postsynaptic density, intracellular component / androgen metabolic process / regulation of glucose metabolic process / estrogen response element binding / response to electrical stimulus / intracellular steroid hormone receptor signaling pathway / core promoter sequence-specific DNA binding / transcription initiation-coupled chromatin remodeling / Hsp70 protein binding / cellular response to transforming growth factor beta stimulus / heat shock protein binding / TBP-class protein binding / steroid binding / cellular response to dexamethasone stimulus / response to activity / synaptic transmission, glutamatergic / female pregnancy / RNA polymerase II transcription regulatory region sequence-specific DNA binding / lung development / Hsp90 protein binding / response to insulin / receptor tyrosine kinase binding / spindle / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / response to calcium ion / circadian rhythm / 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 / DNA-binding transcription activator activity, RNA polymerase II-specific / protein-containing complex assembly / sequence-specific DNA binding / dendritic spine / transcription coactivator activity / nuclear speck / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / centrosome / negative regulation of DNA-templated transcription / glutamatergic synapse / chromatin binding / protein-containing complex binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / 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 / membrane / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Pufall, M.A. / Yamamoto, K.R. / Meijsing, S.H. | ||||||
Citation | Journal: Science / Year: 2009 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3g6r.cif.gz | 118.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3g6r.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 3g6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/3g6r ftp://data.pdbj.org/pub/pdb/validation_reports/g6/3g6r | HTTPS FTP |
---|
-Related structure data
Related structure data | 3fylC 3g6pC 3g6qC 3g6tC 3g6uC 3g8uC 3g8xC 3g97C 3g99C 3g9iC 3g9jC 3g9mC 3g9oC 3g9pC 1gluS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 5556.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: FKBP5 binding site top strand 18bp | ||||
---|---|---|---|---|---|
#2: DNA chain | Mass: 5436.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: FKBP5 binding site bottom strand 18bp | ||||
#3: 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.) Rattus norvegicus (Norway rat) / Gene: Grl, Nr3c1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: P06536 #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.39 % | ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 50mM Na Cacodylate, pH 6.5, 2.25mM Spermine, 18mM MgCl2, 9% Isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.282963 Å |
Detector | Type: ADSC QUANTUM Q315r / Detector: CCD / Date: Apr 26, 2008 |
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.282963 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 19913 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 37.422 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.08 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 1.88 / Num. unique all: 1322 / Rsym value: 0.394 / % possible all: 65 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GLU Resolution: 2.3→49.195 Å / SU ML: 2.14 / σ(F): 0.15 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.377 Å2 / ksol: 0.355 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→49.195 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|