[English] 日本語
Yorodumi- PDB-1r4r: Crystallographic analysis of the interaction of the glucocorticoi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r4r | ||||||
---|---|---|---|---|---|---|---|
Title | Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION/DNA / GR / steroid receptor / protein-DNA complex / glucocorticoid / IR3 / 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 / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Luisi, B.F. / Xu, W.X. / Otwinowski, Z. / Freedman, L.P. / Yamamoto, K.R. / Sigler, P.B. | ||||||
Citation | Journal: Nature / Year: 1991 Title: Crystallographic Analysis of the Interaction of the Glucocorticoid Receptor with DNA Authors: Luisi, B.F. / Xu, W.X. / Otwinowski, Z. / Freedman, L.P. / Yamamoto, K.R. / Sigler, P.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1r4r.cif.gz | 75.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1r4r.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 1r4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/1r4r ftp://data.pdbj.org/pub/pdb/validation_reports/r4/1r4r | HTTPS FTP |
---|
-Related structure data
Related structure data | 1gluSC 1r4oC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 5803.785 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Idealized glucocorticoid response element IR3, top strand | ||
---|---|---|---|
#2: DNA chain | Mass: 5819.784 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Idealized glucocorticoid response element IR3, bottom strand | ||
#3: Protein | Mass: 10232.162 Da / Num. of mol.: 2 / Fragment: DNA binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: NR3C1 OR GRL / Plasmid: pT7 440-525 / Production host: Escherichia coli (E. coli) / References: UniProt: P06536 #4: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 65.82 % |
---|
-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
-Processing
Software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1GLU Resolution: 3→6 Å | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→6 Å
|