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- PDB-8fh0: Crystal structure of mutant Androgen Receptor ligand binding doma... -

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Basic information

Entry
Database: PDB / ID: 8fh0
TitleCrystal structure of mutant Androgen Receptor ligand binding domain H875Y/F877L/T878A with DHT
ComponentsAndrogen receptor
KeywordsGENE REGULATION / AR / Androgen receptor / DHT / steroid 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 / cellular response to steroid hormone stimulus / morphogenesis of an epithelial fold / 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 / Androgen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsDoamekpor, S.K. / Tong, L.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: A partially open conformation of an androgen receptor ligand-binding domain with drug-resistance mutations.
Authors: Doamekpor, S.K. / Peng, P. / Xu, R. / Ma, L. / Tong, Y. / Tong, L.
History
DepositionDec 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)30,4423
Polymers30,0551
Non-polymers3872
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.522, 65.979, 73.136
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: 30055.156 Da / Num. of mol.: 1 / Mutation: H875Y,F877L,T878A
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.4-0.8 M sodium citrate, 0.1 M Hepes pH 7.5, 20% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.59→200 Å / Num. obs: 70466 / % possible obs: 99.7 % / Redundancy: 3.86 % / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.04 / Net I/σ(I): 16.48
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.59-1.690.62113180.820.7221
1.69-1.810.321107490.9430.3771
1.81-1.950.17899920.9850.2051
1.95-2.140.08692020.9950.0991
2.14-2.390.05182850.9970.061
2.39-2.760.03872890.9980.0441
2.76-3.380.03362100.9990.0381
3.38-4.770.02747770.9990.0321
4.77-2000.02626440.9990.031

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Processing

Software
NameVersionClassification
PHENIXv1.2refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→48.99 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 2000 5.38 %
Rwork0.1957 --
obs0.1964 37154 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→48.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 26 108 2101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062050
X-RAY DIFFRACTIONf_angle_d0.9312776
X-RAY DIFFRACTIONf_dihedral_angle_d15.204760
X-RAY DIFFRACTIONf_chiral_restr0.066306
X-RAY DIFFRACTIONf_plane_restr0.01346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.630.29311380.30782426X-RAY DIFFRACTION99
1.63-1.680.27181410.26872482X-RAY DIFFRACTION100
1.68-1.730.27321400.25252471X-RAY DIFFRACTION100
1.73-1.780.31321430.27092499X-RAY DIFFRACTION100
1.78-1.850.26331400.25812465X-RAY DIFFRACTION100
1.85-1.920.23421420.23022488X-RAY DIFFRACTION100
1.92-2.010.23121420.20312496X-RAY DIFFRACTION100
2.01-2.110.24041420.20242494X-RAY DIFFRACTION100
2.11-2.250.25631430.2012502X-RAY DIFFRACTION100
2.25-2.420.2071420.19712510X-RAY DIFFRACTION100
2.42-2.660.20211430.20492524X-RAY DIFFRACTION100
2.66-3.050.20261450.2132536X-RAY DIFFRACTION100
3.05-3.840.19991460.18772579X-RAY DIFFRACTION100
3.84-48.990.18241530.16772682X-RAY DIFFRACTION100

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