+Open data
-Basic information
Entry | Database: PDB / ID: 3g9p | ||||||
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Title | GR DNA binding domain:Sgk 16bp complex-7 | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / glucocorticoid / DNA-binding / allostry / lever arm / hormone / Alternative initiation / Chromatin regulator / Cytoplasm / Lipid-binding / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Receptor / Steroid-binding / Transcription / 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 / steroid hormone binding / nucleus localization / neuroinflammatory response / glucocorticoid metabolic process / hormone binding / 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 / regulation of gluconeogenesis / adrenal gland development / 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 / response to electrical stimulus / nuclear receptor-mediated steroid hormone signaling pathway / core promoter sequence-specific DNA binding / transcription initiation-coupled chromatin remodeling / cellular response to transforming growth factor beta stimulus / heat shock protein binding / Hsp70 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 / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / response to calcium ion / spindle / circadian rhythm / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of neuron apoptotic process / regulation of cell population proliferation / gene expression / protein-containing complex assembly / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / 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 / negative regulation of DNA-templated transcription / centrosome / 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 / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.652 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g9p.cif.gz | 114.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g9p.ent.gz | 85.8 KB | Display | PDB format |
PDBx/mmJSON format | 3g9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g9p_validation.pdf.gz | 440.3 KB | Display | wwPDB validaton report |
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Full document | 3g9p_full_validation.pdf.gz | 444.9 KB | Display | |
Data in XML | 3g9p_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 3g9p_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/3g9p ftp://data.pdbj.org/pub/pdb/validation_reports/g9/3g9p | HTTPS FTP |
-Related structure data
Related structure data | 3fylC 3g6pC 3g6qC 3g6rC 3g6tC 3g6uC 3g8uC 3g8xC 3g97C 3g99C 3g9iC 3g9jC 3g9mC 3g9oC 1gluS C: citing same article (ref.) 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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Unit cell |
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-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: Nr3c1, Grl / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: P06536 #2: DNA chain | | Mass: 4897.203 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Glucocorticoid receptor binding site: Sgk 16 base top strand #3: DNA chain | | Mass: 4897.203 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Glucocorticoid receptor binding site: Sgk 16 base bottom strand #4: Chemical | ChemComp-ZN / #5: 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: 3.08 Å3/Da / Density % sol: 60.01 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 50mM MES, pH 6.0, 20mM MgCl2, 15% isopropanol, 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: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115878 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 12, 2007 |
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115878 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→50 Å / Num. obs: 42923 / % possible obs: 88.2 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 23.068 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.078 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.59→1.65 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1664 / Rsym value: 0.53 / % possible all: 34.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GLU Resolution: 1.652→34.354 Å / SU ML: 1.4 / σ(F): 0.12 / 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: 56.535 Å2 / ksol: 0.36 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.652→34.354 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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