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- PDB-8rm7: Crystal Structure of Human Androgen Receptor DNA Binding Domain B... -

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Basic information

Entry
Database: PDB / ID: 8rm7
TitleCrystal Structure of Human Androgen Receptor DNA Binding Domain Bound to its Response Element: MMTV-177 GRE/ARE
Components
  • Isoform 2 of Androgen receptor
  • MMTV-177 GRE/ARE Chain C
  • MMTV-177 GRE/ARE, Chain D
KeywordsSTRUCTURAL PROTEIN / DBD-DNA binding complex / androgen receptor dna binding domain
Function / homology
Function and homology information


male somatic sex determination / activation of prostate induction by androgen receptor signaling pathway / lateral sprouting involved in mammary gland duct morphogenesis / POU domain binding / negative regulation of integrin biosynthetic process / regulation of developmental growth / male genitalia morphogenesis / positive regulation of integrin biosynthetic process / tertiary branching involved in mammary gland duct morphogenesis / animal organ formation ...male somatic sex determination / activation of prostate induction by androgen receptor signaling pathway / lateral sprouting involved in mammary gland duct morphogenesis / POU domain binding / negative regulation of integrin biosynthetic process / regulation of developmental growth / male genitalia morphogenesis / 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 / intracellular receptor signaling pathway / cellular response to testosterone stimulus / RNA polymerase II general transcription initiation factor binding / positive regulation of transcription by RNA polymerase III / positive regulation of insulin-like growth factor receptor signaling pathway / positive regulation of intracellular estrogen receptor signaling pathway / morphogenesis of an epithelial fold / cellular response to steroid hormone stimulus / seminiferous tubule development / androgen receptor signaling pathway / single fertilization / RUNX2 regulates osteoblast differentiation / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / regulation of protein localization to plasma membrane / intracellular steroid hormone receptor signaling pathway / positive regulation of phosphorylation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / steroid binding / insulin-like growth factor receptor signaling pathway / epithelial cell proliferation / G protein-coupled receptor activity / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of cell differentiation / multicellular organism growth / SUMOylation of intracellular receptors / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / transcription coactivator binding / beta-catenin binding / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / male gonad development / nuclear receptor activity / negative regulation of epithelial cell proliferation / MAPK cascade / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / ATPase binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / positive regulation of MAPK cascade / molecular adaptor activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / signaling receptor binding / chromatin binding / positive regulation of cell population proliferation / chromatin / positive regulation of gene expression / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / 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 / Zinc finger, C4 type (two domains) / 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 ...Androgen receptor / Androgen receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / 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: 2.25 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
C: MMTV-177 GRE/ARE Chain C
D: MMTV-177 GRE/ARE, Chain D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3808
Polymers27,1184
Non-polymers2624
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-30 kcal/mol
Surface area12820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.910, 29.780, 112.609
Angle α, β, γ (deg.)90.00, 124.91, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-114-

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 MMTV-177 GRE/ARE Chain C


Mass: 5538.628 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 MMTV-177 GRE/ARE, Chain D


Mass: 5480.576 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: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.41 Å3/Da / Density % sol: 63.93 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium citrate and 20 %(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 277.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 10, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.25→46.18 Å / Num. obs: 18435 / % possible obs: 100 % / Redundancy: 5.4 % / Biso Wilson estimate: 34.1 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.046 / Rrim(I) all: 0.108 / Χ2: 0.62 / Net I/σ(I): 8.7
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1686 / CC1/2: 0.839 / Rpim(I) all: 0.188 / Rrim(I) all: 0.406 / Χ2: 0.31 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia20.6.0data reduction
Aimless0.7.4data scaling
MOLREP11.7.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→46.17 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 31.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.31 903 4.91 %RANDOM
Rwork0.2671 ---
obs0.2692 18402 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1110 731 4 98 1943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041954
X-RAY DIFFRACTIONf_angle_d0.762770
X-RAY DIFFRACTIONf_dihedral_angle_d24.301789
X-RAY DIFFRACTIONf_chiral_restr0.044299
X-RAY DIFFRACTIONf_plane_restr0.004233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.390.36791410.28912870X-RAY DIFFRACTION100
2.39-2.580.30331370.31572902X-RAY DIFFRACTION100
2.58-2.830.3011520.30592898X-RAY DIFFRACTION100
2.83-3.240.35451580.29282883X-RAY DIFFRACTION100
3.25-4.090.32491580.23472912X-RAY DIFFRACTION100
4.09-46.170.2671570.25163034X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2898-0.4948-0.54950.68860.7430.7344-0.6234-0.2193-0.32490.26380.4330.54630.55580.1683-0.6830.06610.0433-0.0120.24630.09980.4478-7.9904-1.512743.9655
20.9889-0.5145-0.60280.49430.17810.82610.1338-0.59690.2975-0.97060.4651-0.6909-0.41280.43431.43040.8787-0.28720.20730.1584-0.15850.32476.57881.5523.3888
3-0.02810.1061-0.03271.44460.47040.08750.08950.6068-0.0271-1.07230.04570.7438-0.1198-0.60520.01490.5005-0.12310.01150.71610.26550.4338-12.81750.911622.8164
40.8963-0.2005-0.29162.427-0.45160.21280.02560.59380.0541-1.13450.44990.85230.0859-0.49460.30880.3843-0.26190.01610.52170.16750.4782-15.2046-0.52726.1686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid 556 through 628)
2X-RAY DIFFRACTION2(chain 'A' and resid 556 through 628)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 18)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 18)

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