+Open data
-Basic information
Entry | Database: PDB / ID: 3g6u | ||||||
---|---|---|---|---|---|---|---|
Title | GR DNA-binding domain:FKBP5 16bp complex-49 | ||||||
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 / 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 / regulation of gluconeogenesis / cellular response to steroid hormone stimulus / 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 | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 3g6u.cif.gz | 116.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3g6u.ent.gz | 87.7 KB | Display | PDB format |
PDBx/mmJSON format | 3g6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g6u_validation.pdf.gz | 444.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3g6u_full_validation.pdf.gz | 455 KB | Display | |
Data in XML | 3g6u_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 3g6u_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/3g6u ftp://data.pdbj.org/pub/pdb/validation_reports/g6/3g6u | HTTPS FTP |
-Related structure data
Related structure data | 3fylC 3g6pC 3g6qC 3g6rC 3g6tC 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: 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 #2: DNA chain | | Mass: 4953.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: FKBP bottom strand #3: DNA chain | | Mass: 4842.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: FKBP top strand #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: 3.08 Å3/Da / Density % sol: 60.01 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50mM HEPES, pH 7.5, 2.5mM Spermine, 80mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115872 Å |
---|---|
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 8, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115872 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 27530 / % possible obs: 72.6 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 37.84 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.056 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 1.6 / Num. unique all: 2088 / Rsym value: 0.807 / % possible all: 72.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1GLU Resolution: 1.9→34.375 Å / SU ML: 1.45 / σ(F): 0.12 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 82.809 Å2 / ksol: 0.388 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.18 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→34.375 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 |
|