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- PDB-8rm6: Crystal Structure of Human Androgen Receptor DNA Binding Domain B... -

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Basic information

Entry
Database: PDB / ID: 8rm6
TitleCrystal Structure of Human Androgen Receptor DNA Binding Domain Bound to its Response Element: C3(1)ARE
Components
  • C3(1)ARE_Chain C
  • C3(1)ARE_Chain D
  • Isoform 2 of Androgen receptor
KeywordsDNA BINDING PROTEIN / androgen receptor / androgen response elements / dbd binding domain-response element 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 / 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 / androgen receptor signaling pathway / cellular response to estrogen stimulus / mammary gland alveolus development / single fertilization / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / 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 / 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 / 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 / transcription coactivator binding / G protein-coupled receptor activity / beta-catenin binding / multicellular organism growth / Nuclear Receptor transcription pathway / positive regulation of miRNA transcription / 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 / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / molecular adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / in utero embryonic development / 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 / cytosol / cytoplasm
Similarity search - Function
Androgen receptor / Androgen 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 ...Androgen receptor / Androgen 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
Similarity search - Domain/homology
DNA / DNA (> 10) / Androgen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLee, X.Y. / Helsen, C. / Van Eynde, W. / Voet, A. / Claessens, F.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)KU Leuven grant (GOA/19/100) Belgium
CitationJournal: J.Steroid Biochem.Mol.Biol. / Year: 2024
Title: Structural mechanism underlying variations in DNA binding by the androgen receptor.
Authors: Lee, X.Y. / Van Eynde, W. / Helsen, C. / Willems, H. / Peperstraete, K. / De Block, S. / Voet, A. / Claessens, F.
History
DepositionJan 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Isoform 2 of Androgen receptor
A: Isoform 2 of Androgen receptor
D: C3(1)ARE_Chain D
C: C3(1)ARE_Chain C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3818
Polymers27,1194
Non-polymers2624
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-26 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.029, 95.359, 115.353
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2212
Components on special symmetry positions
IDModelComponents
11B-808-

HOH

21B-825-

HOH

31B-827-

HOH

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Components

#1: Protein Isoform 2 of Androgen receptor / Dihydrotestosterone receptor / Nuclear receptor subfamily 3 group C member 4


Mass: 8049.417 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AR, DHTR, NR3C4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10275
#2: DNA chain C3(1)ARE_Chain D


Mass: 5536.599 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: DNA chain C3(1)ARE_Chain C


Mass: 5483.593 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: 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: 3.5 Å3/Da / Density % sol: 64.82 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium hepes pH7.5,15% (w/v) peg 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Feb 14, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.05→49.35 Å / Num. obs: 26537 / % possible obs: 99.9 % / Redundancy: 51.3 % / Biso Wilson estimate: 41.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.239 / Rpim(I) all: 0.033 / Rrim(I) all: 0.242 / Net I/σ(I): 19.9
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 42.8 % / Rmerge(I) obs: 2.509 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1972 / CC1/2: 0.821 / Rpim(I) all: 0.386 / Rrim(I) all: 2.539 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
AimlessCCP4Interface 7.1.018data scaling
XDSDECEMBER 2003 VERSIONdata reduction
PHASERCCP4Interface 7.1.018phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→49.35 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2468 1328 5.02 %
Rwork0.2211 --
obs0.2225 26468 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 731 4 64 1908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091941
X-RAY DIFFRACTIONf_angle_d1.052751
X-RAY DIFFRACTIONf_dihedral_angle_d25.861781
X-RAY DIFFRACTIONf_chiral_restr0.055298
X-RAY DIFFRACTIONf_plane_restr0.007229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.130.33341330.28152724X-RAY DIFFRACTION100
2.13-2.230.2941460.26722740X-RAY DIFFRACTION100
2.23-2.350.24781410.24522751X-RAY DIFFRACTION100
2.35-2.490.27371450.25452773X-RAY DIFFRACTION100
2.49-2.690.27111510.25542775X-RAY DIFFRACTION100
2.69-2.960.24331470.24362759X-RAY DIFFRACTION100
2.96-3.380.24941580.23242789X-RAY DIFFRACTION99
3.38-4.260.24981520.21172834X-RAY DIFFRACTION100
4.26-49.350.22131550.1892995X-RAY DIFFRACTION100

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