+Open data
-Basic information
Entry | Database: PDB / ID: 5cbx | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | AncGR DNA Binding Domain - (+)GRE Complex | ||||||||||||
Components |
| ||||||||||||
Keywords | dna binding protein/dna / DNA binding protein / dna binding protein-dna complex | ||||||||||||
Function / homology | Function and homology information Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / glucocorticoid metabolic process / neuroinflammatory response / microglia differentiation / maternal behavior / mammary gland duct morphogenesis ...Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / glucocorticoid metabolic process / neuroinflammatory response / microglia differentiation / maternal behavior / mammary gland duct morphogenesis / nucleus localization / astrocyte differentiation / cellular response to glucocorticoid stimulus / motor behavior / regulation of gluconeogenesis / adrenal gland development / cellular response to steroid hormone stimulus / estrogen response element binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / intracellular steroid hormone receptor signaling pathway / core promoter sequence-specific DNA binding / cellular response to transforming growth factor beta stimulus / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / TBP-class protein binding / steroid binding / cellular response to dexamethasone stimulus / synaptic transmission, glutamatergic / chromosome segregation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / SUMOylation of intracellular receptors / spindle / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / Regulation of RUNX2 expression and activity / positive regulation of neuron apoptotic process / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / gene expression / chromatin organization / DNA-binding transcription activator activity, RNA polymerase II-specific / Potential therapeutics for SARS / DNA-binding transcription factor activity, RNA polymerase II-specific / mitochondrial matrix / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / cell division / centrosome / negative regulation of DNA-templated transcription / synapse / apoptotic process / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / zinc ion binding / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | unclassified (unknown) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||||||||
Authors | Hudson, W.H. / Ortlund, E.A. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Distal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space. Authors: Hudson, W.H. / Kossmann, B.R. / de Vera, I.M. / Chuo, S.W. / Weikum, E.R. / Eick, G.N. / Thornton, J.W. / Ivanov, I.N. / Kojetin, D.J. / Ortlund, E.A. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5cbx.cif.gz | 114 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5cbx.ent.gz | 82.9 KB | Display | PDB format |
PDBx/mmJSON format | 5cbx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/5cbx ftp://data.pdbj.org/pub/pdb/validation_reports/cb/5cbx | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 11739.622 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unclassified (unknown) / Gene: NR3C1, GRL / Production host: Escherichia coli (E. coli) / References: UniProt: P04150*PLUS #2: DNA chain | Mass: 5540.604 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) #3: DNA chain | Mass: 5466.553 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | Sequence details | This sequence was generated from ancestral sequence reconstruction | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.38 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES (pH 7.5), 12% PEG 20000, and 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 22, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 57251 / % possible obs: 95.4 % / Redundancy: 3 % / Net I/σ(I): 14.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2→33.326 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.74 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→33.326 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|