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- PDB-1t63: Crystal Structure of the Androgen Receptor Ligand Binding Domain ... -

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Basic information

Entry
Database: PDB / ID: 1t63
TitleCrystal Structure of the Androgen Receptor Ligand Binding Domain with DHT and a peptide derived from its physiological coactivator GRIP1 NR box3
Components
  • Androgen receptor
  • Nuclear receptor coactivator 2
KeywordsHORMONE/GROWTH FACTOR / androgen receptor ligand binding domain GRIP1 NR boxes coactivators DHT crystal structure / HORMONE-GROWTH FACTOR COMPLEX
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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / 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 / Synthesis of bile acids and bile salts / cellular response to estrogen stimulus / mammary gland alveolus development / single fertilization / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / transcription regulator inhibitor activity / positive regulation of phosphorylation / regulation of protein localization to plasma membrane / RNA polymerase II core promoter sequence-specific DNA binding / cellular response to hormone stimulus / Recycling of bile acids and salts / intracellular receptor signaling pathway / estrogen receptor signaling pathway / positive regulation of adipose tissue development / steroid binding / : / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / insulin-like growth factor receptor signaling pathway / SUMOylation of transcription cofactors / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Activation of gene expression by SREBF (SREBP) / response to progesterone / epithelial cell proliferation / nuclear receptor binding / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of smoothened signaling pathway / positive regulation of cell differentiation / SUMOylation of intracellular receptors / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / molecular condensate scaffold activity / Transcriptional activation of mitochondrial biogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / transcription coactivator binding / PPARA activates gene expression / G protein-coupled receptor activity / Cytoprotection by HMOX1 / beta-catenin binding / multicellular organism growth / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / positive regulation of miRNA transcription / RNA polymerase II transcription regulator complex / 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 / HATs acetylate histones / ATPase binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / molecular adaptor activity / transcription regulator complex
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
5-ALPHA-DIHYDROTESTOSTERONE / Androgen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsEstebanez-Perpina, E. / Moore, J.M.R. / Mar, E. / Nguyen, P. / Delgado-Rodrigues, E. / Baxter, J.D. / Webb, P. / Fletterick, R.J. / Guy, R.K.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The Molecular Mechanisms of Coactivator Utilization in Ligand-dependent Transactivation by the Androgen Receptor.
Authors: Estebanez-Perpina, E. / Moore, J.M.R. / Mar, E. / Delgado-Rodrigues, E. / Nguyen, P. / Baxter, J.D. / Buehrer, B.M. / Webb, P. / Fletterick, R.J. / Guy, R.K.
History
DepositionMay 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 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: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2773
Polymers30,9862
Non-polymers2901
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-10 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.490, 67.370, 70.520
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 / Fragment: AR ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AR, NR3C4, DHTR / Production host: Escherichia coli (E. coli) / References: UniProt: P10275
#2: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Transcriptional intermediary factor 2


Mass: 1708.931 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOA2, TIF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15596
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.157 Å3/Da / Density % sol: 43.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: hepes, Na-citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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 4 / Detector: CCD / Date: Jul 2, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.07→24.36 Å / Num. all: 15915 / Num. obs: 15915 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.3 Å2
Reflection shellHighest resolution: 2.07 Å / % possible all: 97.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→24.36 Å / Isotropic thermal model: throughout / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.23 779 random
Rwork0.2 --
all-15915 -
obs-15915 -
Displacement parametersBiso mean: 38.8 Å2
Baniso -1Baniso -2Baniso -3
1-7.63 Å20 Å20 Å2
2---3 Å20 Å2
3----4.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.07→24.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 21 124 2307
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d18.5
X-RAY DIFFRACTIONc_improper_angle_d0.91

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