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- PDB-2nw4: Crystal Structure of the Rat Androgen Receptor Ligand Binding Dom... -

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Basic information

Entry
Database: PDB / ID: 2nw4
TitleCrystal Structure of the Rat Androgen Receptor Ligand Binding Domain Complex with BMS-564929
ComponentsAndrogen receptor
KeywordsHORMONE/GROWTH FACTOR / ANDROGEN RECEPTOR / STEROID RECEPTOR / NUCLEAR RECEPTOR / TRANSCRIPTION REGULATION / LIGAND-BINDING DOMAIN / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


reproductive behavior / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / copulation / male sex differentiation / skeletal muscle hypertrophy / positive regulation of penile erection / regulation of prostatic bud formation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ribonucleotide binding / reproductive system development ...reproductive behavior / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / copulation / male sex differentiation / skeletal muscle hypertrophy / positive regulation of penile erection / regulation of prostatic bud formation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ribonucleotide binding / reproductive system development / male courtship behavior / Ub-specific processing proteases / male somatic sex determination / activation of prostate induction by androgen receptor signaling pathway / lateral sprouting involved in mammary gland duct morphogenesis / SUMOylation of intracellular receptors / POU domain binding / negative regulation of integrin biosynthetic process / regulation of developmental growth / reproductive structure development / male genitalia morphogenesis / positive regulation of integrin biosynthetic process / Nuclear Receptor transcription pathway / tertiary branching involved in mammary gland duct morphogenesis / animal organ formation / cellular response to follicle-stimulating hormone stimulus / 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 / fertilization / RNA polymerase II general transcription initiation factor binding / 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 / nuclear androgen receptor binding / cellular response to steroid hormone stimulus / morphogenesis of an epithelial fold / response to testosterone / seminiferous tubule development / androgen receptor signaling pathway / 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 / steroid binding / insulin-like growth factor receptor signaling pathway / epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of cell differentiation / response to insulin / multicellular organism growth / transcription coactivator binding / positive regulation of miRNA transcription / beta-catenin binding / negative regulation of epithelial cell proliferation / nuclear receptor activity / male gonad development / MAPK cascade / response to estradiol / positive regulation of NF-kappaB transcription factor activity / ATPase binding / regulation of gene expression / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / positive regulation of MAPK cascade / molecular adaptor activity / transcription cis-regulatory region binding / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of cell population proliferation / axon / signaling receptor binding / negative regulation of DNA-templated transcription / dendrite / chromatin binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding
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 / Zinc finger, C4 type (two domains) / 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 / Zinc finger, C4 type (two domains) / 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
Chem-8NH / Androgen receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 3 Å
AuthorsOstrowski, J. / Kuhns, J.E. / Lupisella, J.A. / Manfredi, M.C. / Beehler, B.C. / Krystek, S.R. / Bi, Y. / Sun, C. / Seethala, R. / Golla, R. ...Ostrowski, J. / Kuhns, J.E. / Lupisella, J.A. / Manfredi, M.C. / Beehler, B.C. / Krystek, S.R. / Bi, Y. / Sun, C. / Seethala, R. / Golla, R. / Sleph, P.G. / Fura, A. / An, Y. / Kish, K.F. / Sack, J.S. / Mookhtiar, K.A. / Grover, G.J. / Hamann, L.G.
CitationJournal: Endocrinology / Year: 2007
Title: Pharmacological and x-ray structural characterization of a novel selective androgen receptor modulator: potent hyperanabolic stimulation of skeletal muscle with hypostimulation of prostate in rats.
Authors: Ostrowski, J. / Kuhns, J.E. / Lupisella, J.A. / Manfredi, M.C. / Beehler, B.C. / Krystek, S.R. / Bi, Y. / Sun, C. / Seethala, R. / Golla, R. / Sleph, P.G. / Fura, A. / An, Y. / Kish, K.F. / ...Authors: Ostrowski, J. / Kuhns, J.E. / Lupisella, J.A. / Manfredi, M.C. / Beehler, B.C. / Krystek, S.R. / Bi, Y. / Sun, C. / Seethala, R. / Golla, R. / Sleph, P.G. / Fura, A. / An, Y. / Kish, K.F. / Sack, J.S. / Mookhtiar, K.A. / Grover, G.J. / Hamann, L.G.
History
DepositionNov 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Androgen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5882
Polymers30,2821
Non-polymers3061
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.640, 65.620, 70.830
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


Mass: 30282.414 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ar, Nr3c4 / Plasmid: PET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P15207
#2: Chemical ChemComp-8NH / 2-CHLORO-4-[(7R,7AS)-7-HYDROXY-1,3-DIOXOTETRAHYDRO-1H-PYRROLO[1,2-C]IMIDAZOL-2(3H)-YL]-3-METHYLBENZONITRILE


Mass: 305.716 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12ClN3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.34 Å3/Da / Density % sol: 42.36 %
Crystal growMethod: vapor diffusion, hanging drop
Details: 0.88M NA TARTRATE, 0.1M NA HEPES, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 24, 2002 / Details: "BLUE" CONFOCAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. obs: 5527 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 13
Reflection shellResolution: 3→3.11 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 3.4 / % possible all: 98.5

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Processing

Software
NameClassification
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
RefinementMethod to determine structure: molecular replacement
Starting model: 1I37

1i37


Resolution: 3→18.2 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 895069.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.293 304 5.5 %RANDOM
Rwork0.249 ---
obs-5481 99.8 %-
Displacement parametersBiso mean: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1-21.8 Å20 Å20 Å2
2---10.31 Å20 Å2
3----11.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 3→18.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 21 8 2031
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.009
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.4
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d20.5
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d1.05
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it1.291.5
X-RAY DIFFRACTIONo_mcangle_it2.272
X-RAY DIFFRACTIONo_scbond_it1.812
X-RAY DIFFRACTIONo_scangle_it2.862.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 51 5.8 %
Rwork0.272 832 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4bms-564929.parbms-564929.top

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