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Yorodumi- PDB-1xq3: Crystal structure of the human androgen receptor ligand binding d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xq3 | ||||||
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Title | Crystal structure of the human androgen receptor ligand binding domain bound with R1881 | ||||||
Components | androgen receptor | ||||||
Keywords | TRANSCRIPTION / crystal structure / human androgen receptor ligand binding domain / R1881 | ||||||
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 / 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 ...male somatic sex determination / activation of prostate induction by androgen receptor signaling pathway / lateral sprouting involved in mammary gland duct morphogenesis / 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 / positive regulation of epithelial cell proliferation involved in prostate gland development / prostate gland epithelium morphogenesis / intracellular receptor signaling pathway / cellular response to testosterone stimulus / positive regulation of transcription by RNA polymerase III / 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 / morphogenesis of an epithelial fold / cellular response to steroid hormone stimulus / seminiferous tubule development / single fertilization / androgen receptor signaling pathway / RUNX2 regulates osteoblast differentiation / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / regulation of protein localization to plasma membrane / intracellular steroid hormone receptor signaling pathway / positive regulation of phosphorylation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / steroid binding / insulin-like growth factor receptor signaling pathway / epithelial cell proliferation / G protein-coupled receptor activity / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of cell differentiation / multicellular organism growth / SUMOylation of intracellular receptors / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / transcription coactivator binding / beta-catenin binding / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / male gonad development / nuclear receptor activity / negative regulation of epithelial cell proliferation / MAPK cascade / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / ATPase binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of MAPK cascade / transcription by RNA polymerase II / molecular adaptor activity / transcription cis-regulatory region binding / 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 / chromatin / positive regulation of gene expression / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | He, B. / Gampe Jr., R.T. / Kole, A.J. / Hnat, A.T. / Stanley, T.B. / An, G. / Stewart, E.L. / Kalman, R.I. / Minges, J.T. / Wilson, E.M. | ||||||
Citation | Journal: Mol.Cell / Year: 2004 Title: Structural basis for androgen receptor interdomain and coactivator interactions suggests a transition in nuclear receptor activation function dominance Authors: He, B. / Gampe Jr., R.T. / Kole, A.J. / Hnat, A.T. / Stanley, T.B. / An, G. / Stewart, E.L. / Kalman, R.I. / Minges, J.T. / Wilson, E.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xq3.cif.gz | 64.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xq3.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 1xq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/1xq3 ftp://data.pdbj.org/pub/pdb/validation_reports/xq/1xq3 | HTTPS FTP |
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-Related structure data
Related structure data | 1xowSC 2ao6C 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: 29046.074 Da / Num. of mol.: 1 / Fragment: ligand binding domain Source method: isolated from a genetically manipulated source Details: inhibited by r1881 / Source: (gene. exp.) Homo sapiens (human) Description: human AR LBD (663-919) with thrombin cleavable NH2-terminal HIS tag Gene: Ar, Nr3c4 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / 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: 2.33 Å3/Da / Density % sol: 46.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100mM BTP, 0.6-1.2M LiSO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 11, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 13364 / Num. obs: 13364 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 326.8 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1245 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XOW.pdb Resolution: 2.25→50 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 270372.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.5516 Å2 / ksol: 0.370965 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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