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- PDB-2qpy: AR LBD with small molecule -

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Basic information

Entry
Database: PDB / ID: 2qpy
TitleAR LBD with small molecule
Components
  • Androgen receptor
  • Coactivator peptide
KeywordsDNA BINDING PROTEIN / androgen receptor DHT coactivator / DNA-binding / Lipid-binding / Metal-binding / Nucleus / Steroid-binding / Transcription / Transcription regulation / Ubl conjugation / Zinc / Zinc-finger
Function / homology
Function and homology information


RUNX2 regulates osteoblast differentiation / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / SUMOylation of intracellular receptors / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / Nuclear Receptor transcription pathway / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / regulation of prostatic bud formation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand ...RUNX2 regulates osteoblast differentiation / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / SUMOylation of intracellular receptors / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / Nuclear Receptor transcription pathway / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / regulation of prostatic bud formation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Endogenous sterols / HATs acetylate histones / male somatic sex determination / prostate induction / lateral sprouting involved in mammary gland duct morphogenesis / male genitalia morphogenesis / reproductive system development / POU domain binding / negative regulation of integrin biosynthetic process / regulation of developmental growth / positive regulation of integrin biosynthetic process / reproductive structure development / tertiary branching involved in mammary gland duct morphogenesis / Regulation of lipid metabolism by PPARalpha / animal organ formation / Cytoprotection by HMOX1 / androgen binding / Leydig cell differentiation / regulation of systemic arterial blood pressure / epithelial cell morphogenesis / Estrogen-dependent gene expression / 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 / Ub-specific processing proteases / membraneless organelle assembly / fertilization / 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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / morphogenesis of an epithelial fold / positive regulation of intracellular estrogen receptor signaling pathway / seminiferous tubule development / locomotor rhythm / aryl hydrocarbon receptor binding / androgen receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / cellular response to estrogen stimulus / mammary gland alveolus development / single fertilization / 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 / positive regulation of adipose tissue development / steroid binding / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / insulin-like growth factor receptor signaling pathway / response to progesterone / epithelial cell proliferation / nuclear receptor binding / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of cell differentiation / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / molecular condensate scaffold activity / transcription coactivator binding / beta-catenin binding / multicellular organism growth / positive regulation of miRNA transcription / RNA polymerase II transcription regulator complex / nuclear receptor activity / circadian rhythm / male gonad development / negative regulation of epithelial cell proliferation / positive regulation of NF-kappaB transcription factor activity / MAPK cascade / ATPase binding / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / gene expression / spermatogenesis / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / in utero embryonic development / transcription by RNA polymerase II / transcription coactivator activity / transcription cis-regulatory region binding / positive regulation of MAPK cascade / protein dimerization activity / nuclear speck / nuclear body
Similarity search - Function
Androgen receptor / Androgen receptor / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator ...Androgen receptor / Androgen receptor / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / : / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / 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
Chem-4HY / 5-ALPHA-DIHYDROTESTOSTERONE / Androgen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsEstebanez-Perpina, E. / Fletterick, R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: A surface on the androgen receptor that allosterically regulates coactivator binding.
Authors: Estebanez-Perpina, E. / Arnold, L.A. / Arnold, A.A. / Nguyen, P. / Rodrigues, E.D. / Mar, E. / Bateman, R. / Pallai, P. / Shokat, K.M. / Baxter, J.D. / Guy, R.K. / Webb, P. / Fletterick, R.J.
History
DepositionJul 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Source and taxonomy / Structure summary
Category: entity / pdbx_entity_src_syn / software
Item: _entity.pdbx_description / _software.classification / _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: Coactivator peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4554
Polymers30,5432
Non-polymers9122
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.790, 66.680, 72.080
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: 29277.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ar, Nr3c4 / Production host: Escherichia coli (E. coli) / References: UniProt: P19091
#2: Protein/peptide Coactivator peptide


Mass: 1265.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q61026*PLUS
#3: Chemical ChemComp-DHT / 5-ALPHA-DIHYDROTESTOSTERONE


Mass: 290.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30O2 / Comment: hormone*YM
#4: Chemical ChemComp-4HY / [4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID


Mass: 621.932 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H9I3O4 / Comment: hormone*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growMethod: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. all: 11046 / Num. obs: 9407 / Rmerge(I) obs: 0.093
Reflection shellHighest resolution: 2.5 Å

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Processing

Software
NameClassification
ELVESrefinement
CNSrefinement
ELVESdata reduction
ELVESdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→100 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.269 -
Rwork0.269 -
obs0.269 9407
all-11046
Refinement stepCycle: LAST / Resolution: 2.5→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2117 0 42 24 2183

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