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Open data
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Basic information
Entry | Database: PDB / ID: 4oed | ||||||
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Title | Crystal structure of AR-LBD bound with co-regulator peptide | ||||||
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![]() | HORMONE RECEPTOR/PEPTIDE / Alpha-helix / Hormone/growth Factor Receptor / Phosphorylation / HORMONE RECEPTOR-PEPTIDE complex | ||||||
Function / homology | ![]() 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 / positive regulation of androgen receptor activity / RNA polymerase II general transcription initiation factor binding / U2-type catalytic step 2 spliceosome / 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 / morphogenesis of an epithelial fold / seminiferous tubule development / androgen receptor signaling pathway / RUNX2 regulates osteoblast differentiation / 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 / positive regulation of phosphorylation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / steroid binding / mRNA Splicing - Major Pathway / insulin-like growth factor receptor signaling pathway / molecular condensate scaffold activity / nuclear receptor coactivator activity / epithelial cell proliferation / nuclear receptor binding / negative regulation of extrinsic apoptotic signaling pathway / G protein-coupled receptor activity / positive regulation of cell differentiation / spliceosomal complex / SUMOylation of intracellular receptors / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / multicellular organism growth / transcription coactivator binding / positive regulation of miRNA transcription / beta-catenin binding / mRNA splicing, via spliceosome / Nuclear Receptor transcription pathway / negative regulation of epithelial cell proliferation / nuclear receptor activity / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / 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 / chromatin / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, J.S. / Hsu, C.L. / Wu, W.G. | ||||||
![]() | ![]() Title: Identification of a new androgen receptor (AR) co-regulator BUD31 and related peptides to suppress wild-type and mutated AR-mediated prostate cancer growth via peptide screening and X-ray structure analysis. Authors: Hsu, C.L. / Liu, J.S. / Wu, P.L. / Guan, H.H. / Chen, Y.L. / Lin, A.C. / Ting, H.J. / Pang, S.T. / Yeh, S.D. / Ma, W.L. / Chen, C.J. / Wu, W.G. / Chang, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.6 KB | Display | ![]() |
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PDB format | ![]() | 47.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4oeaSC ![]() 4oeyC ![]() 4oezC ![]() 4ofrC ![]() 4ofuC ![]() 4oghC ![]() 4oh5C ![]() 4oh6C ![]() 4ohaC ![]() 4oilC ![]() 4oiuC ![]() 4oj9C ![]() 4ojbC ![]() 4ok1C ![]() 4okbC ![]() 4oktC ![]() 4okwC ![]() 4okxC ![]() 4olmC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29088.086 Da / Num. of mol.: 1 / Fragment: ligand binding domain / Mutation: R760A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 2017.396 Da / Num. of mol.: 1 / Fragment: UNP residues 56-70 / Mutation: I70Y / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-DHT / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6M magnesium sulphate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→50 Å / Num. all: 6688 / Num. obs: 6664 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4OEA Resolution: 2.79→25.34 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.893 / SU B: 19.05 / SU ML: 0.368 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.493 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.342 Å2
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Refinement step | Cycle: LAST / Resolution: 2.79→25.34 Å
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Refine LS restraints |
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