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- PDB-8gl7: AncAR1 - progesterone - Tif2 -

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Basic information

Entry
Database: PDB / ID: 8gl7
TitleAncAR1 - progesterone - Tif2
Components
  • Ancestral androgen receptor
  • Nuclear receptor coactivator 2
KeywordsSIGNALING PROTEIN / Androgen receptor / nuclear receptor / progesterone / transcription factor
Function / homology
Function and homology information


RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol ...RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / response to progesterone / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / Circadian Clock / HATs acetylate histones / Estrogen-dependent gene expression / transcription regulator complex / transcription coactivator activity / nuclear body / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
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 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 / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
PROGESTERONE / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLittle, M.M. / Ortlund, E.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R56DK115213 United States
CitationJournal: To Be Published
Title: Evolutionary tuning of a key helix drove androgen selectivity
Authors: Little, M.M. / Ortlund, E.A.
History
DepositionMar 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ancestral androgen receptor
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5124
Polymers30,1052
Non-polymers4072
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-5 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.714, 69.714, 144.439
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Ancestral androgen receptor


Mass: 28998.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1106.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-STR / PROGESTERONE


Mass: 314.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 4000, 0.1M Tris pH 8.9, 4% glycerol

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.37209→49.3 Å / Num. obs: 14581 / % possible obs: 96.961 % / Redundancy: 22.5 % / Biso Wilson estimate: 32.88 Å2 / CC1/2: 0.99 / CC star: 0.998 / Rpim(I) all: 0.088 / Rrim(I) all: 0.423 / Χ2: 0.713 / Net I/σ(I): 1.77
Reflection shellResolution: 2.4→2.486 Å / Num. unique obs: 4584 / CC1/2: 0.726 / Rpim(I) all: 0.411 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PDB-REDOrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→49.3 Å / SU ML: 0.2221 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.2043
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2527 722 5.03 %
Rwork0.1973 13635 -
obs0.1999 14357 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.75 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2113 0 29 56 2198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112191
X-RAY DIFFRACTIONf_angle_d0.99162965
X-RAY DIFFRACTIONf_chiral_restr0.0502333
X-RAY DIFFRACTIONf_plane_restr0.0094368
X-RAY DIFFRACTIONf_dihedral_angle_d5.0692288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.590.27431410.24252617X-RAY DIFFRACTION97.01
2.59-2.850.28111400.23092638X-RAY DIFFRACTION98.06
2.85-3.260.31891430.22562709X-RAY DIFFRACTION98.62
3.26-4.10.2591450.18782765X-RAY DIFFRACTION99.22
4.1-49.30.20211530.16912906X-RAY DIFFRACTION99.03
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)
12.43680913870.32648908693-0.04930691090471.03023885509-0.1839798959082.022187620.0289168010669-0.197731954256-0.2886899813340.113820549287-0.0538900631874-0.2274894243510.07354215841740.1708823188094.48030393424E-50.2141734651990.0202988058258-0.01282489559220.222705601357-0.01221881127850.23994260613-0.00376666384413-30.924300531720.7983616254
21.861492305830.431088185901-0.213340111292.330115848330.9073066264152.40941084037-0.0166508034670.0835113335262-0.170975158079-0.0496821456990.0935267980942-0.01425473109080.157854194207-0.02456712417435.36876486072E-50.183065207290.020063785236-0.01147810538730.2164712616440.0128773796060.195565893186-5.18485940065-32.567553309210.6425912021
32.722261393961.019487397840.8442372917292.27253335346-0.9501479781031.53147709116-0.0212516288634-0.0380287299960.420053243079-0.2716852531430.117441722004-0.382853422652-0.2468425512570.3270427301940.01516956656610.255137558877-0.0498602780989-0.01430041977190.3079506796570.04624432392220.2658489462884.07990087481-14.19021108377.0021141905
41.68624353639-0.4758648056590.1184600311241.792436946520.09984480105680.5308951599950.005196920019660.07707723747610.06179411083250.002187369538090.04327863572580.117958629403-0.103257476018-0.06011472755120.002702639266980.193197213584-0.0315057165988-0.02793590436810.297079012803-0.008600507069320.257078932892-11.1347407838-23.444041343213.7260268855
50.424986892259-0.2130968413360.2976009405570.125714112761-0.1962638880980.3929239936540.289683381653-0.03761596695420.8509365370730.354635574774-0.0992387776082-0.189995911285-0.2788779280440.814968779042-0.00885148169290.2854119002870.00675835548804-0.0006302069593930.333319505842-0.0488544406880.3563662475631.18491106097-19.316253135831.205032516
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 672 through 729 )AA672 - 7293 - 60
22chain 'A' and (resid 730 through 813 )AA730 - 81361 - 144
33chain 'A' and (resid 814 through 848 )AA814 - 848145 - 179
44chain 'A' and (resid 849 through 916 )AA849 - 916180 - 247
55chain 'D' and (resid 743 through 751 )DD743 - 7511 - 9

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