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- PDB-7zu2: Crystal structure of mutant AR-LBD (Q799E) bound to dihydrotestos... -

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Basic information

Entry
Database: PDB / ID: 7zu2
TitleCrystal structure of mutant AR-LBD (Q799E) bound to dihydrotestosterone
ComponentsAndrogen receptor
KeywordsDNA BINDING PROTEIN / Hormone Receptor / Nuclear Receptor / DHT Receptor
Function / homology
Function and homology information


male somatic sex determination / prostate induction / lateral sprouting involved in mammary gland duct morphogenesis / male genitalia morphogenesis / regulation of developmental growth / POU domain binding / 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 / regulation of developmental growth / POU domain binding / 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 / positive regulation of epithelial cell proliferation involved in prostate gland development / prostate gland epithelium morphogenesis / prostate gland growth / 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 / morphogenesis of an epithelial fold / cellular response to steroid hormone stimulus / positive regulation of intracellular estrogen receptor signaling pathway / androgen receptor signaling pathway / seminiferous tubule development / RUNX2 regulates osteoblast differentiation / nuclear steroid receptor activity / 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 / RNA polymerase II transcription regulatory region sequence-specific DNA binding / 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 / beta-catenin binding / Nuclear Receptor transcription pathway / positive regulation of miRNA transcription / transcription coactivator binding / multicellular organism growth / male gonad development / nuclear receptor activity / negative regulation of epithelial cell proliferation / cell-cell signaling / MAPK cascade / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / molecular adaptor activity / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / 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 / cytoplasm / cytosol
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
5-ALPHA-DIHYDROTESTOSTERONE / IMIDAZOLE / Androgen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsAlegre-Marti, A. / Jimenez-Panizo, A. / Estebanez-Perpina, E. / Fuentes-Prior, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2023
Title: A hotspot for posttranslational modifications on the androgen receptor dimer interface drives pathology and anti-androgen resistance.
Authors: Alegre-Marti, A. / Jimenez-Panizo, A. / Martinez-Tebar, A. / Poulard, C. / Peralta-Moreno, M.N. / Abella, M. / Anton, R. / Chinas, M. / Eckhard, U. / Piulats, J.M. / Rojas, A.M. / Fernandez- ...Authors: Alegre-Marti, A. / Jimenez-Panizo, A. / Martinez-Tebar, A. / Poulard, C. / Peralta-Moreno, M.N. / Abella, M. / Anton, R. / Chinas, M. / Eckhard, U. / Piulats, J.M. / Rojas, A.M. / Fernandez-Recio, J. / Rubio-Martinez, J. / Le Romancer, M. / Aytes, A. / Fuentes-Prior, P. / Estebanez-Perpina, E.
History
DepositionMay 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)29,4764
Polymers29,0471
Non-polymers4293
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, immunoprecipitation, mass spectrometry, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint5 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.514, 66.043, 72.424
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 29047.059 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
#2: Chemical ChemComp-DHT / 5-ALPHA-DIHYDROTESTOSTERONE


Mass: 290.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: ammonium acetate tris sodium formate spermidine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.74 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2020
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74 Å / Relative weight: 1
ReflectionResolution: 1.74→44.59 Å / Num. obs: 28510 / % possible obs: 100 % / Redundancy: 5.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.039 / Rrim(I) all: 0.089 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.74-1.775.22.153818415590.3371.0422.3981.5100
9.04-44.554.50.03211142460.9980.0170.03736.799.1

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T7T

1t7t


Resolution: 1.74→44.59 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.289 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 1433 5 %RANDOM
Rwork0.1828 ---
obs0.1847 27029 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 106.02 Å2 / Biso mean: 37.235 Å2 / Biso min: 22 Å2
Baniso -1Baniso -2Baniso -3
1-2.16 Å20 Å2-0 Å2
2---1.28 Å20 Å2
3----0.89 Å2
Refinement stepCycle: final / Resolution: 1.74→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1981 0 31 64 2076
Biso mean--32.06 41.88 -
Num. residues----242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122068
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.6222795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2575240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.60722110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3615368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4851513
X-RAY DIFFRACTIONr_chiral_restr0.1040.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021532
LS refinement shellResolution: 1.74→1.785 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 119 -
Rwork0.303 1954 -
all-2073 -
obs--100 %

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