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Yorodumi- PDB-1e3g: Human Androgen Receptor Ligand Binding in complex with the ligand... -
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-Basic information
Entry | Database: PDB / ID: 1e3g | |||||||||
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Title | Human Androgen Receptor Ligand Binding in complex with the ligand metribolone (R1881) | |||||||||
Components | ANDROGEN RECEPTOR | |||||||||
Keywords | ANDROGEN RECEPTOR / HUMAN ANDROGEN RECEPTOR / LIGAND BINDING DOMAIN | |||||||||
Function / homology | Function and homology information male somatic sex determination / activation of prostate induction by androgen receptor signaling pathway / lateral sprouting involved in mammary gland duct morphogenesis / morphogenesis of an epithelial fold / POU domain binding / negative regulation of integrin biosynthetic process / regulation of developmental growth / male genitalia morphogenesis / positive regulation of integrin biosynthetic process / tertiary branching involved in mammary gland duct morphogenesis ...male somatic sex determination / activation of prostate induction by androgen receptor signaling pathway / lateral sprouting involved in mammary gland duct morphogenesis / morphogenesis of an epithelial fold / POU domain binding / negative regulation of integrin biosynthetic process / regulation of developmental growth / male genitalia morphogenesis / positive regulation of integrin biosynthetic process / tertiary branching involved in mammary gland duct morphogenesis / animal organ formation / androgen binding / Leydig cell differentiation / regulation of systemic arterial blood pressure / epithelial cell morphogenesis / prostate gland growth / epithelial cell differentiation involved in prostate gland development / non-membrane-bounded organelle assembly / positive regulation of epithelial cell proliferation involved in prostate gland development / prostate gland epithelium morphogenesis / intracellular receptor signaling pathway / cellular response to testosterone stimulus / RNA polymerase II general transcription initiation factor binding / positive regulation of insulin-like growth factor receptor signaling pathway / positive regulation of intracellular estrogen receptor signaling pathway / positive regulation of transcription by RNA polymerase III / cellular response to steroid hormone stimulus / seminiferous tubule development / androgen receptor signaling pathway / RUNX2 regulates osteoblast differentiation / positive regulation of phosphorylation / single fertilization / mammary gland alveolus development / regulation of protein localization to plasma membrane / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / epithelial cell proliferation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / steroid binding / insulin-like growth factor receptor signaling pathway / positive regulation of miRNA transcription / molecular condensate scaffold activity / SUMOylation of intracellular receptors / negative regulation of extrinsic apoptotic signaling pathway / G protein-coupled receptor activity / positive regulation of cell differentiation / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Nuclear Receptor transcription pathway / multicellular organism growth / transcription coactivator binding / nuclear receptor activity / beta-catenin binding / negative regulation of epithelial cell proliferation / male gonad development / MAPK cascade / cell-cell signaling / ATPase binding / positive regulation of NF-kappaB transcription factor activity / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription cis-regulatory region binding / transcription by RNA polymerase II / positive regulation of MAPK cascade / molecular adaptor activity / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / signaling receptor binding / chromatin binding / positive regulation of cell population proliferation / positive regulation of gene expression / positive regulation of DNA-templated transcription / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Matias, P.M. / Donner, P. / Coelho, R. / Thomaz, M. / Peixoto, C. / Macedo, S. / Otto, N. / Joschko, S. / Scholz, P. / Wegg, A. ...Matias, P.M. / Donner, P. / Coelho, R. / Thomaz, M. / Peixoto, C. / Macedo, S. / Otto, N. / Joschko, S. / Scholz, P. / Wegg, A. / Basler, S. / Schafer, M. / Ruff, M. / Egner, U. / Carrondo, M.A. | |||||||||
Citation | Journal: J. Biol. Chem. / Year: 2000 Title: Structural evidence for ligand specificity in the binding domain of the human androgen receptor. Implications for pathogenic gene mutations. Authors: Matias, P.M. / Donner, P. / Coelho, R. / Thomaz, M. / Peixoto, C. / Macedo, S. / Otto, N. / Joschko, S. / Scholz, P. / Wegg, A. / Basler, S. / Schafer, M. / Egner, U. / Carrondo, M.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e3g.cif.gz | 66.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e3g.ent.gz | 47.3 KB | Display | PDB format |
PDBx/mmJSON format | 1e3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e3g_validation.pdf.gz | 669.4 KB | Display | wwPDB validaton report |
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Full document | 1e3g_full_validation.pdf.gz | 678.3 KB | Display | |
Data in XML | 1e3g_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 1e3g_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/1e3g ftp://data.pdbj.org/pub/pdb/validation_reports/e3/1e3g | HTTPS FTP |
-Related structure data
Related structure data | 1e3kC 1a28S S: Starting model for refinement C: citing same article (ref.) |
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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: 30664.869 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN RESIDUES 447-709 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10275 |
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#2: Chemical | ChemComp-R18 / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.4 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8.5 Details: RESERVOIR SOLUTION: 0.4M NA2HPO4-2(H2O), 0.4M K2HPO4, 0.1M TRIS-HCL PH 8.5, 0.1M (NH4)2HPO4 AND 5% PEG200. DROPS WERE COMPOSED OF EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTION AND WERE SET ...Details: RESERVOIR SOLUTION: 0.4M NA2HPO4-2(H2O), 0.4M K2HPO4, 0.1M TRIS-HCL PH 8.5, 0.1M (NH4)2HPO4 AND 5% PEG200. DROPS WERE COMPOSED OF EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTION AND WERE SET UP USING THE SITTING DROP METHOD. | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.932 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 15, 1999 / Details: TOROIDAL MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.932 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→24.4 Å / Num. obs: 10638 / % possible obs: 99.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 49.4 Å2 / Rmerge(I) obs: 0.078 |
Reflection shell | Resolution: 2.4→2.46 Å / Rmerge(I) obs: 0.351 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 37443 |
Reflection shell | *PLUS % possible obs: 99.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A28 Resolution: 2.4→24.4 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY MAPS
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Displacement parameters | Biso mean: 45.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 25 Å / Luzzati sigma a obs: 0.47 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→24.4 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.21 / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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