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Yorodumi- PDB-2amb: Crystal structure of human androgen receptor ligand binding domai... -
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-Basic information
Entry | Database: PDB / ID: 2amb | ||||||
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Title | Crystal structure of human androgen receptor ligand binding domain in complex with tetrahydrogestrinone | ||||||
Components | Androgen receptor | ||||||
Keywords | Hormone/Growth Factor Receptor / Nuclear Receptor / Androgen Receptor / Ligand Binding Domain / THG / Agonist / Designer Androgen / Hormone-Growth Factor Receptor 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 / 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 transcription by RNA polymerase III / positive regulation of intracellular estrogen receptor signaling pathway / cellular response to steroid hormone stimulus / morphogenesis of an epithelial fold / seminiferous tubule development / androgen receptor signaling pathway / RUNX2 regulates osteoblast differentiation / single fertilization / 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 / molecular condensate scaffold activity / G protein-coupled receptor activity / positive regulation of cell differentiation / negative regulation of extrinsic apoptotic signaling pathway / SUMOylation of intracellular receptors / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / multicellular organism growth / beta-catenin binding / transcription coactivator binding / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / nuclear receptor activity / negative regulation of epithelial cell proliferation / male gonad development / 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 / transcription by RNA polymerase II / positive regulation of MAPK cascade / 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 / chromatin / positive regulation of cell population proliferation / positive regulation of gene expression / positive regulation of DNA-templated transcription / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Pereira de Jesus-Tran, K. / Cote, P.-L. / Cantin, L. / Blanchet, J. / Labrie, F. / Breton, R. | ||||||
Citation | Journal: Protein Sci. / Year: 2006 Title: Comparison of crystal structures of human androgen receptor ligand-binding domain complexed with various agonists reveals molecular determinants responsible for binding affinity. Authors: Pereira de Jesus-Tran, K. / Cote, P.-L. / Cantin, L. / Blanchet, J. / Labrie, F. / Breton, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2amb.cif.gz | 75.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2amb.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 2amb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/2amb ftp://data.pdbj.org/pub/pdb/validation_reports/am/2amb | HTTPS FTP |
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-Related structure data
Related structure data | 2am9C 2amaSC C: citing same article (ref.) S: Starting model for refinement |
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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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Details | The biological assembly is a monomer |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 30996.188 Da / Num. of mol.: 1 / Fragment: ligand binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AR, DHTR, NR3C4 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P10275 |
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-Non-polymers , 6 types, 197 molecules
#2: Chemical | ChemComp-SO4 / |
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#3: Chemical | ChemComp-17H / |
#4: Chemical | ChemComp-DTT / |
#5: Chemical | ChemComp-EPE / |
#6: Chemical | ChemComp-GOL / |
#7: 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: 1.92 Å3/Da / Density % sol: 35.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Na/K tartrate. MgSO4, Hepes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 10, 2004 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→19.3 Å / Num. all: 25459 / Num. obs: 25459 / % possible obs: 94.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Biso Wilson estimate: 29.449 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.059 / Net I/σ(I): 18.01 |
Reflection shell | Resolution: 1.75→1.8 Å / % possible obs: 63.8 % / Redundancy: 2 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 3.01 / Num. measured obs: 2765 / Num. unique all: 1358 / Num. unique obs: 1358 / Rsym value: 0.288 / % possible all: 63.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AMA Resolution: 1.75→19.3 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 57.687 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.542 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: 0.26 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→19.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.024
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Xplor file |
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