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Yorodumi- PDB-1glu: CRYSTALLOGRAPHIC ANALYSIS OF THE INTERACTION OF THE GLUCOCORTICOI... -
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-Basic information
Entry | Database: PDB / ID: 1glu | ||||||
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Title | CRYSTALLOGRAPHIC ANALYSIS OF THE INTERACTION OF THE GLUCOCORTICOID RECEPTOR WITH DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / 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 / Resolution: 2.9 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1glu.cif.gz | 72.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1glu.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 1glu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1glu_validation.pdf.gz | 384.7 KB | Display | wwPDB validaton report |
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Full document | 1glu_full_validation.pdf.gz | 447.7 KB | Display | |
Data in XML | 1glu_validation.xml.gz | 13 KB | Display | |
Data in CIF | 1glu_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/1glu ftp://data.pdbj.org/pub/pdb/validation_reports/gl/1glu | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: LYS A 435 - PRO A 436 OMEGA ANGLE = 121.694 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATIO |
-Components
#1: DNA chain | Mass: 5804.773 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 9133.866 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER Gene (production host): GENE FRAGMENT (AMINO ACIDS 440 TO 525) Production host: Escherichia coli (E. coli) / References: UniProt: P06536 #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Sequence details | THE FIRST SIX AMINO ACID RESIDUES ARE CLONAL LINKERS, THEY ARE DIFFERENT FROM THE NATURAL SEQUENCE. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 66.89 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 281 K / Method: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, temperature 281.00K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 8 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 263 K |
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Diffraction source | Source: ROTATING ANODE |
Detector | Type: SDMS / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.196 / Rfactor obs: 0.196 / Highest resolution: 2.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.9 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 6.5 Å / Num. reflection obs: 7669 / Rfactor obs: 0.196 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.4 |