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. Author manuscript; available in PMC: 2024 May 7.
Published in final edited form as: Mol Cell. 2023 May 19;83(12):2091–2107.e7. doi: 10.1016/j.molcel.2023.04.025
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Monoclonal ANTI-FLAG M2-HRP antibody Sigma-Aldrich Cat# A8592; RRID: AB_439702
Chemicals, peptides, and recombinant proteins
TRIS SRL Cat# 71033
HEPES SRL Cat# 63732
NaCl SRL Cat# 41721
EDTA SRL Cat# 12070
Phenylmethanesulfonyl Fluoride (PMSF) SRL Cat# 84375 (84375)
Benzamidine Hydrochloride SRL Cat# 93014 (0248255)
Lysozyme SRL Cat# 45822
Glycerol SRL Cat# 77453
Dithiothreitol HiMedia Cat# MB070
Lauryl Maltose Neopentyl Glycol (MNG) Anatrace Cat# NG310, CAS no.1257852-96-2
Paraformaldehyde (PFA) Sigma Aldrich Cat# P6148, CAS no. 30525-89-4
Poly-D-lysine Sigma Aldrich Cat# P0899
TMB (Tetramethylbenzidine) Thermo Fisher Scientific Cat# 34028
Janus Green B Sigma Aldrich Cat# 201677
PEI (Polyethylenimine) Polysciences Cat# 23966
Bovine Serum Albumin, BSA SRL Cat# 83803 (0140105)
HBSS - Hank’s Balanced Salt Solution Thermo Fisher Scientific Cat# 14065
GIBCO Fetal Bovine Serum Thermo Fisher Scientific Cat# 10270-106
DMEM Cellclone Cat# CC3004
Phosphate-buffered saline (PBS) Sigma Aldrich Cat# D1283
GIBCO Penicillin-Streptomycin Thermo Fisher Scientific Cat# 15140122
Coelenterazine Goldbio Cat# CZ05
Glyco-diosgenin (GDN) Anatrace GDN101
Cholesteryl Hemisuccinate Sigma C6512
Coomassie briliiant Blue SRL Cat# 64222
Uranyl formate Polysciences Cat# 24762-1
Recombinant rat β-arrestin1 Purified N/A
Recombinant bovine β-arrestin2 Purified N/A
C5aR1pp1 Chemically synthesized N/A
C5aR1pp2 Chemically synthesized N/A
C5aR1pp3 Chemically synthesized N/A
V2Rpp Chemically synthesized N/A
CXCR4pp1 Chemically synthesized N/A
CXCR4pp2 Chemically synthesized N/A
CXCR4pp3 Chemically synthesized N/A
CXCR4pp4 Chemically synthesized N/A
Recombinant human C5a Purified N/A
Bradykinin Genscript N/A
Arginine Vasopressin Peptide (AVP) Genscript N/A
Uranyl formate Polysciences Cat# 24762-1
Formvar/carbon coated 300 mesh
copper grids
PELCO (Ted Pella) Cat# 01753-F
Critical commercial assays
Site directed mutagenesis kit NEB Cat# E0554
NanoBiT assay Promega N/A
Deposited data
C5aR1pp-βarr1-Fab30 This study PDB: 8GO8, EMD-34173
V2Rpp-βarr2-Fab30 This study PDB: 8GOC, EMD-34175
C5aR1pp-βarr2-Fab30 This study PDB: 8GOO, EMD-34178
CXCR4pp-βarr1-Fab30 This study PDB: 8GP3, EMD-34188
C5aR1pp-βarr1-Fab30-Local-refine This study PDB: 8I0N, EMD-35104
V2Rpp-βarr2-Fab30-Local-refine This study PDB: 8I10, EMD-35115
C5aR1pp-βarr2-Fab30-Local-refine This study PDB: 8I0Z, EMD-35114
CXCR4pp-βarr1-Fab30-Local-refine This study PDB: 8I0Q, EMD-35106
Experimental models: Cell lines
Human: HEK293 ATCC Cat# CRL-3216
Oligonucleotides
C5aR1_R-insertion SDM primer Forward:
CGCTCCACAGTGGACACTATGG
This study N/A
C5aR1_R-insertion SDM primer Reverse:
GCGCGTGAATGACTTGCT
This study N/A
B2Rmut Forward:
AACACGGACCTCCATCTCCGTG
This study N/A
B2RmutReverse
GTCATGGAGTTCTCCATCTGAATGGG
This study N/A
M2Rmut_Forward:
AAGTCTACTTCACTGGGCCAC
This study N/A
M2Rmut_Reverse:
GACGGTGTTTTCGTCCTG
This study N/A
β-arrestin2 Double mutant (βarr2DM)
Fw: ggcgAACAACCGTGAAAAACGTG
This study N/A
β-arrestin2 Double mutant (βarr2DM)
Rv: aggaaCGGGGTGATGGTGTAAAC
This study N/A
Recombinant DNA
PcDNA_3.1 (empty vector) Dr. Arun K Shukla N/A
pcDNA3.1_V2R-WT Dr. Arun K Shukla N/A
pcDNA3.1_C5aR1-WT Dr. Arun K Shukla N/A
pcDNA3.1_CXCR3-WT Dr. Arun K Shukla N/A
pcDNA3.1_CXCR7-WT Dr. Arun K Shukla N/A
pcDNA3.1_B2R-WT Dr. Arun K Shukla N/A
pcDNA3.1_M2R-WT Dr. Arun K Shukla N/A
pcDNA3.1_C5aR1-mutTRRST This study N/A
pcDNA3.1_B2R-mutΔG368/L370T Dr. Arun K Shukla N/A
pcDNA3.1_M2R-mutTVKST This study N/A
pCAGGS_V2R-WT-SmBiT Dr. Arun K Shukla N/A
pCAGGS _C5aR1-SmBiT Dr. Arun K Shukla N/A
pCAGGS_SmBiT-βarr2WT Dr. Asuka Inoue N/A
pCAGGS_SmBiT-βarr2DM This study N/A
pCAGGS_LgBiT-βarr2WT Dr. Asuka Inoue N/A
pCAGGS_LgBiT-βarr2DM This study N/A
pCAGGS_LgBiT-FYVE Dr. Asuka Inoue N/A
pCAGGS_LgBiT-Ib30 Dr. Asuka Inoue N/A
Software and algorithms
UCSF Chimera Pettersen et al.64 https://www.cgl.ucsf.edu/chimera/
UCSF Chimera X Pettersen et al.65 https://www.rbvi.ucsf.edu/chimerax/
COOT Emsley et al.66 https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
cryoSPARC Punjani et al.67 https://cryosparc.com/
PDBsum Laskowski et al.68 http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/
Phenix Liebschner et al.69 https://www.phenix-online.org/
PyMol Schrodinger https://pymol.org/2/
Prism 8 GraphPad Software https://www.graphpad.com/scientific-software/prism/
Relion3.1.2 Zivanov et al.70 https://www3.mrc-lmb.cam.ac.uk/relion/index.php?title=Main_Page
SerialEM Mastronarde71 https://bio3d.colorado.edu/SerialEM/
Graphpad Prism 9 GraphPad Software, San Diego, California USA https://www.graphpad.com/scientific-software/prism/
ImageJ Schneider et al.72 https://imagej.nih.gov/ij/download.html