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- PDB-2q7k: The Androgen Receptor Prostate Cancer Mutant H874Y Ligand Binding... -

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Basic information

Entry
Database: PDB / ID: 2q7k
TitleThe Androgen Receptor Prostate Cancer Mutant H874Y Ligand Binding Domain Bound with Testosterone and an AR 20-30 Peptide
Components(Androgen receptor) x 2
KeywordsHORMONE / androgen receptor prostate cancer mutant H874Y ligand binding domain / testoseterone / N-terminal AR peptide
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 / negative regulation of integrin biosynthetic process / regulation of developmental growth / positive regulation of integrin biosynthetic process / tertiary branching involved in mammary gland duct morphogenesis / animal organ formation ...male somatic sex determination / prostate induction / lateral sprouting involved in mammary gland duct morphogenesis / male genitalia morphogenesis / POU domain binding / negative regulation of integrin biosynthetic process / regulation of developmental growth / 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 / cellular response to testosterone stimulus / 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 / morphogenesis of an epithelial fold / cellular response to steroid hormone stimulus / positive regulation of intracellular estrogen receptor signaling pathway / seminiferous tubule development / RUNX2 regulates osteoblast differentiation / androgen receptor signaling pathway / cellular response to estrogen stimulus / mammary gland alveolus development / single fertilization / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of phosphorylation / regulation of protein localization to plasma membrane / RNA polymerase II core promoter sequence-specific DNA binding / 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 / SUMOylation of intracellular receptors / molecular condensate scaffold activity / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / transcription coactivator binding / G protein-coupled receptor activity / beta-catenin binding / multicellular organism growth / Nuclear Receptor transcription pathway / positive regulation of miRNA transcription / nuclear receptor activity / male gonad development / negative regulation of epithelial cell proliferation / positive regulation of NF-kappaB transcription factor activity / 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
TESTOSTERONE / Androgen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGampe, R.T.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Modulation of androgen receptor activation function 2 by testosterone and dihydrotestosterone.
Authors: Askew, E.B. / Gampe, R.T. / Stanley, T.B. / Faggart, J.L. / Wilson, E.M.
History
DepositionJun 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3May 8, 2013Group: Structure summary
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Androgen receptor
B: Androgen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8726
Polymers31,3002
Non-polymers5734
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.932, 66.117, 70.681
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Androgen receptor / Dihydrotestosterone receptor


Mass: 30032.121 Da / Num. of mol.: 1 / Mutation: H874Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AR, DHTR, NR3C4 / Production host: Escherichia coli (E. coli) / References: UniProt: P10275
#2: Protein/peptide Androgen receptor / Dihydrotestosterone receptor


Mass: 1267.413 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AR, DHTR, NR3C4 / Production host: Escherichia coli (E. coli) / References: UniProt: P10275

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Non-polymers , 4 types, 174 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TES / TESTOSTERONE


Mass: 288.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28O2 / Comment: hormone*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.09 Å3/Da / Density % sol: 41.06 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→42.72 Å / Num. obs: 23750 / % possible obs: 98.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.42 / Net I/σ(I): 41.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2142 / % possible all: 87.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→42.72 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.516 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20856 790 3.2 %RANDOM
Rwork0.18023 ---
obs0.18112 23750 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.692 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2029 0 37 170 2236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222151
X-RAY DIFFRACTIONr_bond_other_d0.0010.021984
X-RAY DIFFRACTIONr_angle_refined_deg1.0671.972921
X-RAY DIFFRACTIONr_angle_other_deg0.7534608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4385260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.77923.95896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49315374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5271511
X-RAY DIFFRACTIONr_chiral_restr0.060.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022327
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02449
X-RAY DIFFRACTIONr_nbd_refined0.2150.2504
X-RAY DIFFRACTIONr_nbd_other0.1660.21968
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21064
X-RAY DIFFRACTIONr_nbtor_other0.080.21087
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7221.51328
X-RAY DIFFRACTIONr_mcbond_other0.1261.5513
X-RAY DIFFRACTIONr_mcangle_it1.12922068
X-RAY DIFFRACTIONr_scbond_it1.4873949
X-RAY DIFFRACTIONr_scangle_it2.3254.5847
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 38 -
Rwork0.237 1493 -
obs--85.2 %

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