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- PDB-4olm: Crystal structure of W741L-AR-LBD bound with co-regulator peptide -

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Basic information

Entry
Database: PDB / ID: 4olm
TitleCrystal structure of W741L-AR-LBD bound with co-regulator peptide
Components
  • Androgen receptor
  • co-regulator peptide
KeywordsHORMONE RECEPTOR/PEPTIDE / Alpha-helix / Hormone/growth Factor Receptor / Phosphorylation / HORMONE RECEPTOR-PEPTIDE complex
Function / homology
Function and homology information


male somatic sex determination / prostate induction / lateral sprouting involved in mammary gland duct morphogenesis / male genitalia morphogenesis / POU domain binding / regulation of developmental growth / positive regulation of integrin biosynthetic process / tertiary branching involved in mammary gland duct morphogenesis / animal organ formation / androgen binding ...male somatic sex determination / prostate induction / lateral sprouting involved in mammary gland duct morphogenesis / male genitalia morphogenesis / POU domain binding / regulation of developmental growth / positive regulation of integrin biosynthetic process / tertiary branching involved in mammary gland duct morphogenesis / animal organ formation / androgen binding / cellular response to testosterone stimulus / regulation of systemic arterial blood pressure / Leydig cell differentiation / epithelial cell differentiation involved in prostate gland development / prostate gland growth / positive regulation of epithelial cell proliferation involved in prostate gland development / prostate gland epithelium morphogenesis / epithelial cell morphogenesis / membraneless organelle assembly / 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 / cellular response to steroid hormone stimulus / morphogenesis of an epithelial fold / positive regulation of intracellular estrogen receptor signaling pathway / seminiferous tubule development / RUNX2 regulates osteoblast differentiation / nuclear steroid receptor activity / androgen receptor signaling pathway / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / single fertilization / RNA polymerase II core promoter sequence-specific DNA binding / regulation of protein localization to plasma membrane / intracellular receptor signaling pathway / estrogen receptor signaling pathway / steroid binding / insulin-like growth factor receptor signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of cell differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / molecular condensate scaffold activity / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / transcription coactivator binding / beta-catenin binding / Nuclear Receptor transcription pathway / positive regulation of miRNA transcription / multicellular organism growth / nuclear receptor activity / male gonad development / negative regulation of epithelial cell proliferation / MAPK cascade / cell-cell signaling / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / molecular adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / in utero embryonic development / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / positive regulation of MAPK cascade / Ub-specific processing proteases / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / signaling receptor binding / negative regulation of cell population proliferation / positive regulation of cell population proliferation / chromatin binding / positive regulation of gene expression / chromatin / 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
Androgen receptor / Androgen receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors ...Androgen receptor / Androgen receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
R-BICALUTAMIDE / Androgen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLiu, J.S. / Hsu, C.L. / Wu, W.G.
CitationJournal: Mol Oncol / Year: 2014
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
DepositionJan 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Androgen receptor
B: co-regulator peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8873
Polymers30,4572
Non-polymers4301
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-7 kcal/mol
Surface area11090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.076, 66.131, 67.732
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Androgen receptor / Dihydrotestosterone receptor / Nuclear receptor subfamily 3 group C member 4


Mass: 29015.035 Da / Num. of mol.: 1 / Fragment: ligand binding doamin / Mutation: W741L, R760A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AR, DHTR, NR3C4 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: P10275
#2: Protein/peptide co-regulator peptide


Mass: 1441.505 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-198 / R-BICALUTAMIDE / (2R)-N-[4-CYANO-3-(TRIFLUOROMETHYL)PHENYL]-3-[(4-FLUOROPHENYL)SULFONYL]-2-HYDROXY-2-METHYLPROPANAMIDE


Mass: 430.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14F4N2O4S / Comment: medication, hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.86 %

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 8861 / Num. obs: 8016 / % possible obs: 90.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.125

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4OJB

4ojb


Resolution: 2.8→25.93 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.901 / SU B: 21.483 / SU ML: 0.421 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31255 287 4.7 %RANDOM
Rwork0.253 ---
all0.253 6160 --
obs0.25585 5873 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.234 Å2
Baniso -1Baniso -2Baniso -3
1-126.52 Å20 Å20 Å2
2---85.74 Å2-0 Å2
3----40.78 Å2
Refinement stepCycle: LAST / Resolution: 2.8→25.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 29 13 2054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192108
X-RAY DIFFRACTIONr_bond_other_d0.0020.022016
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9672857
X-RAY DIFFRACTIONr_angle_other_deg0.81634616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0965249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15323.36798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.61715362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9921513
X-RAY DIFFRACTIONr_chiral_restr0.0770.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212340
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02525
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.507 23 -
Rwork0.418 409 -
obs--98.41 %

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