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. Author manuscript; available in PMC: 2024 Dec 7.
Published in final edited form as: Structure. 2023 Sep 19;31(12):1545–1555.e9. doi: 10.1016/j.str.2023.08.020
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
LanthaScreen Tb-anti-GST Antibody Thermo Fisher Scientific Cat#PV3550
Bacterial and virus strains
TurboCells BL21 (DE3) Competent E. coli Genlantis Cat#C302020
Chemicals, peptides, and recombinant proteins
Dimethyl sulfoxide Thermo Fisher Scientific Cat#BP231-100
T0901317 Cayman Chemical Cat#71810
Rosiglitazone MedChemExpress Cat#HY-17386
GW0742 MedChemExpress Cat#HY-13928
SJPYT-299 This paper N/A
SJPYT-300 This paper N/A
SJPYT-301 This paper N/A
SJPYT-302 Lin et al.27 N/A
SJPYT-303 This paper N/A
SJPYT-304 This paper N/A
SJPYT-305 This paper N/A
SJPYT-315 Lin et al.27 N/A
SJPYT-316 Lin et al.27 N/A
SJPYT-317 Lin et al.27 N/A
SJPYT-318 This paper N/A
SJPYT-319 Lin et al.27 N/A
SJPYT-320 This paper N/A
Dulbecco's Modified Eagle's Medium (DMEM) ATCC Cat#30-2002
RPMI-1640 Medium ATCC Cat#30-2001
Leibovitz's L-15 Medium ATCC Cat#30-2008
DMEM, high glucose, HEPES, no phenol red Thermo Fisher Scientific Cat#21063029
Fetal bovine serum (FBS), Canadian Origin Cytiva Cat#SH30396.03
HyClone Charcoal/Dextran treated FBS, US Origin Cytiva Cat#SH30068.03
Hygromycin B (50 mg/mL) Thermo Fisher Scientific Cat#10687010
Zeocin Selection Reagent Thermo Fisher Scientific Cat#R25001
Geneticin Selective Antibiotic (G418 Sulfate) (50 mg/mL) Thermo Fisher Scientific Cat#10131027
Matrigel Growth Factor Reduced Basement Membrane Matrix Corning Cat#356230
Sodium Pyruvate (100 mM) Thermo Fisher Scientific Cat#11360070
MEM Non-Essential Amino Acids Solution (100X) Thermo Fisher Scientific Cat#11140050
NEBuilder HiFi DNA Assembly Master Mix New England Biolabs Cat#E2621S
KpnI-HF New England Biolabs Cat#R3142S
FAM-SRC1-B Peptide: FAM-(PEG)5-CPSSHSSLTERHKILHRLLQEGSPS-NH2 Lin et al.46 N/A
Magnesium chloride, 1M aq. soln., sterile-filtered Thermo Fisher Scientific Cat#J62411AD
Bovine Serum Albumin Sigma-Aldrich Cat#A3294
Ethylenediamine Tetraacetic Acid (EDTA) Thermo Fisher Scientific E478-500
Isopropanol Thermo Fisher Scientific Cat#A416-4
Ethylene glycol Sigma-Aldrich Cat#102466-500ML
Pluronic F-127, 0.2 μm filtered (10% Solution in Water) Thermo Fisher Scientific Cat#P6866
Lysozyme, Egg White Gold Biotechnology Cat#12650-88-3
Terrific Broth, Modified, Granulated, 5 Kilograms Research Products International Cat#T15100-5000.0
D-(+)-Glucose Sigma-Aldrich Cat#G8270
SIGMAFAST Protease Inhibitor Cocktail Tablets, EDTA-Free Sigma-Aldrich Cat#S8830
IPTG Gold Biotechnology Cat#I2481C100
Ampicillin (Sodium), USP Grade Gold Biotechnology Cat#A-301-100
DTT (Dithiothreitol) (> 99% pure) Protease free Gold Biotechnology Cat#DTT100
Tris Base Ultra Pure [Tris (Hydroxymethyl) Aminomethane] Research Products International Cat#T60040-1000.0
Sodium Chloride Research Products International Cat#S23020-500.0
Glycerol, 99+%, extra pure Thermo Fisher Scientific Cat#158920025
Imidazole, 99% Thermo Fisher Scientific Cat#122025000
HisTrap FF Cytiva Cat#17525501
HiLoad 26/600 Superdex 200 pg Cytiva Cat#28989336
FuGENE HD Transfection Reagent Promega Cat#E2311
ProxiPlate-384 Plus F, Black 384-shallow well Microplate PerkinElmer Cat#6008260
CulturPlate-384, White Opaque 384-well Microplate, Sterile and Tissue Culture Treated PerkinElmer Cat#6007680
PXR (SXR) Ligand Binding Domain Protein Thermo Fisher Scientific Cat#PV4841
LXR-a Recombinant Human Protein, Ligand Binding Domain, GST-Tagged Thermo Fisher Scientific Cat#PV4657
LXR-b Recombinant Human Protein, Ligand Binding Domain, GST-Tagged Thermo Fisher Scientific Cat#PV4660
His-tagged PXR LBD This paper N/A
Unlabeled SRC-1 Peptide: N-CPSSHSSLTERHKILHRLLQEGSPS-C This paper N/A
Critical commercial assays
CellTiter-Glo Luminescent Cell Viability Assay Promega Cat#G7572
steadylite plus Reporter Gene Assay System PerkinElmer Cat#6066751
LiveBLAzer FRET-B/G Loading Kit with CCF4-AM Thermo Fisher Scientific Cat#K1096
Maxwell 16 LEV simplyRNA Tissue Kit Promega Cat#AS1280
SuperScript VILO cDNA Synthesis Kit Thermo Fisher Scientific Cat#11754050
TaqMan Fast Advanced Master Mix Thermo Fisher Scientific Cat#4444557
TaqMan gene expression assay for CYP3A4 Thermo Fisher Scientific Cat#Hs00604506_m1
TaqMan gene expression assay for ABCA1 Thermo Fisher Scientific Cat#Hs01059118_m1
TaqMan gene expression assay for GAPDH Thermo Fisher Scientific Cat#Hs03929097_g1
TaqMan gene expression assay for RNA18S Thermo Fisher Scientific Cat#Hs03928990_g1
Deposited data
Crystal structure of PXR LBD bound to SJPYT-318 This paper PDB ID 8SZV
Experimental models: Cell lines
293T/17 Cells ATCC Cat#CRL-11268
GeneBLAzer LXRα-UAS-bla HEK 293T Cells Thermo Fisher Scientific Cat#K1692
GeneBLAzer LXRβ-UAS-bla HEK 293T Cells Thermo Fisher Scientific Cat#K1699
GeneBLAzer PPARδ-UAS-bla HEK 293T Cells Thermo Fisher Scientific Cat#K1690
GeneBLAzer PPARγ-UAS-bla HEK 293H Cells Thermo Fisher Scientific Cat#K1701
SNU-C4 Cells Korean Cell Line Bank Cat#0000C4
SNU81 Cells Korean Cell Line Bank Cat#00081
SNU719 Cells Korean Cell Line Bank Cat#00719
LS1034 Cells ATCC Cat#CRL-2158
SNU620 Cells Korean Cell Line Bank Cat#00620
SW948 Cells ATCC Cat#CCL-237
SW1417 Cells ATCC Cat#CCL-238
SW1463 Cells ATCC Cat#CCL-234
Oligonucleotides
5’-TCTAGAGCGGCCGCAGGTACCAGTGAACGGACAGGGACTC-3’ Integrated DNA Technologies N/A
5’-GGCCTTAGTTATTCAGGTACCTCAGCTACCTGTGATGCC-3’ Integrated DNA Technologies N/A
Recombinant DNA
pG5luc Promega Cat#E2440
pBIND Promega Cat#E2440
pETDuet-1-PXR LBD-mSRC-1 Lin et al.32 N/A
pcDNA3-FLAG-PXR Lin et al.45 N/A
pBIND-PXR LBD This paper N/A
pBIND-FXR LBD This paper N/A
pBIND-RORγ LBD This paper N/A
Software and algorithms
XDS Kabsch48 https://xds.mr.mpg.de/
Phenix Liebschner et al.52 https://phenix-online.org/
Coot Emsley et al.51 http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
PyMOL Schrödinger https://pymol.org/2/
Prism 9 Graphpad Software https://www.graphpad.com/features