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Yorodumi- PDB-1t65: Crystal structure of the androgen receptor ligand binding domain ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t65 | ||||||
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Title | Crystal structure of the androgen receptor ligand binding domain with DHT and a peptide derived form its physiological coactivator GRIP1 NR box 2 bound in a non-helical conformation | ||||||
Components |
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Keywords | HORMONE/GROWTH FACTOR / androgen receptor ligand binding domain GRIP1 NR box2 coactivators crystal structure non-helical / HORMONE-GROWTH FACTOR COMPLEX | ||||||
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 / RNA polymerase II general transcription initiation factor binding / positive regulation of insulin-like growth factor receptor signaling pathway / positive regulation of transcription by RNA polymerase III / positive regulation of intracellular estrogen receptor signaling pathway / morphogenesis of an epithelial fold / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / cellular response to steroid hormone stimulus / seminiferous tubule development / androgen receptor signaling pathway / RUNX2 regulates osteoblast differentiation / single fertilization / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / regulation of protein localization to plasma membrane / intracellular steroid hormone receptor signaling pathway / positive regulation of phosphorylation / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / steroid binding / Regulation of lipid metabolism by PPARalpha / insulin-like growth factor receptor signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / response to progesterone / epithelial cell proliferation / G protein-coupled receptor activity / nuclear receptor binding / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of cell differentiation / circadian regulation of gene expression / multicellular organism growth / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / positive regulation of miRNA transcription / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / negative regulation of epithelial cell proliferation / MAPK cascade / Circadian Clock / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / HATs acetylate histones / ATPase binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / in utero embryonic development / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / positive regulation of MAPK cascade / transcription coactivator activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Estebanez-Perpina, E. / Moore, J.M.R. / Mar, E. / Nguyen, P. / Delgado-Rodrigues, E. / Baxter, J.D. / Webb, P. / Fletterick, R.J. / Guy, R.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: The Molecular Mechanisms of Coactivator Utilization in Ligand-dependent Transactivation by the Androgen Receptor. Authors: Estebanez-Perpina, E. / Moore, J.M.R. / Mar, E. / Delgado-Rodrigues, E. / Nguyen, P. / Baxter, J.D. / Buehrer, B.M. / Webb, P. / Fletterick, R.J. / Guy, R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t65.cif.gz | 72.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t65.ent.gz | 53.3 KB | Display | PDB format |
PDBx/mmJSON format | 1t65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/1t65 ftp://data.pdbj.org/pub/pdb/validation_reports/t6/1t65 | HTTPS FTP |
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-Related 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: 29277.340 Da / Num. of mol.: 1 / Fragment: AR Ligand Binding Domain 669-919 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AR, NR3C4, DHTR / Production host: Escherichia coli (E. coli) / References: UniProt: P10275 |
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#2: Protein/peptide | Mass: 1579.866 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NCOA2, TIF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15596 |
#3: Chemical | ChemComp-DHT / |
#4: 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: 2.116 Å3/Da / Density % sol: 41.93 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: hepes, Na-citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→24.2 Å / Num. all: 29066 / Num. obs: 29066 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.1 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→24.2 Å / Isotropic thermal model: restrained / Cross valid method: throught / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 25.4 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.17 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→24.2 Å
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Refine LS restraints |
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