REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit “Peroxidase Anti-Peroxidase soluble complex”	Sigma	P1291; RRID:AB_1079562
Sheep anti-Mcm7	Maric et. al, 2014	N/A
Sheep anti-Mcm3	Maric et. al, 2014	N/A
Goat anti-Mcm2	Santa Cruz	sc-9839; RRID:AB_648841
Sheep anti-Mcm5	Maric et. al, 2014	N/A
Sheep anti-Mcm6	Maric et. al, 2014	N/A
Sheep anti-Mrc1	This study	N/A
Sheep anti-Ctf4	Maric et. al, 2014	N/A
Sheep anti-Csm3	Maric et. al, 2014	N/A
Sheep anti-Cdc45	Maric et. al, 2014	N/A
Sheep anti-Psf1	Maric et. al, 2014	N/A
Sheep anti-Psf3	Maric et. al, 2014	N/A
Sheep anti-Sld5	Maric et. al, 2014	N/A
Rabbit anti-FLAG	Sigma-Aldrich	F7425; RRID:AB_439687
Rabbit anti-Cdc53	Santacruz	sc-50444; RRID:AB_1121399
Mouse monoclonal anti-FLAG (M2)	Sigma-Aldrich	F1804; RRID:AB_262044
Mouse monoclonal anti-polyubiquitylated conjugates (FK2)	Enzo Life Sciences	BML-PW8810; RRID:AB_10541840
Bacterial and Virus Strains
Escherichia coli: BL21-CodonPlus (DE3)-RIL	Agilent	230245
Chemicals, Peptides, and Recombinant Proteins
Indole-3-acetic acid sodium salt	Sigma-Aldrich	I5148
Ni-NTA agarose	QIAGEN	30210
Roche Complete EDTA-free protease inhibitor cocktail	Roche	000000011873580001
Recombinant human Ubiquitin	MRC PPU Reagents and Services	DU20027
Recombinant Cdc48 (wt and E315A E588A mutant)	This study	N/A
Recombinant Ufd1-Npl4	This study	N/A
Recombinant Shp1	This study	N/A
Recombinant Uba1	This study	N/A
Recombinant Cdc34	This study	N/A
Recombinant FLAG-Ubiquitin	MRC PPU Reagents and Services	DU46789
Recombinant Propargyl-Ubiquitin	MRC PPU Reagents and Services	DU49003
Recombinant K0 human Ubiquitin	MRC PPU Reagents and Services	DU24363
Recombinant human USP2	MRC PPU Reagents and Services	DU13025
Experimental Models: Organisms/Strains
S. cerevisiae strains are detailed in Table S1		N/A
Recombinant DNA
Plasmid: 14His-SMT3-Cdc48	Stein et al., 2014	N/A
Plasmid: 14His-SMT3-cdc48-E315A 588A	This study	N/A
Plasmid: pRS305-GAL-Mcm7-5FLAG9His	This study	N/A
Plasmid: pRS305-GAL-Mcm7-K29A-5FLAG9His	This study	N/A
Plasmid: pRS306-GAL-ProteinA-3TEV-Dia2(1-724)	This study	N/A
Software and Algorithms
FlowJo	TreeStar Inc.	https://www.flowjo.com