REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit polyclonal anti-IFITM3 antibody	Proteintech	Cat#11714-1-AP; RRID: AB_2295684
Rabbit polyclonal anti-UBXD1 antibody	Proteintech	Cat#14706-1-AP; RRID: AB_2210488
Rabbit polyclonal anti-p47 antibody	Proteintech	Cat#15620-1-AP
Rabbit polyclonal anti-GAPDH antibody HRP-conjugated	Proteintech	Cat#HRP-60004; RRID: AB_2737588
Rabbit polyclonal anti-Tubulin antibody HRP-conjugated	Proteintech	Cat#HRP-66031
VCP monoclonal antibody (5)	ThermoFisher Scientific	Cat#MA3-004; RRID: AB_2214638
Mono- and polyubiquitinylated conjugates, mAb (FK2H) (HRP conjugate) antibody	Enzo Life Sciences	Cat#BML-PW0150; RRID: AB_10554460
Anti-HA-Peroxidase; Rat monoclonal antibody (clone 3F10) conjugated with peroxidase	Roche	Cat#12013819001; RRID: AB_390917
Anti-c-myc-Peroxidase; Mouse monoclonal antibody (clone 9E10) conjugated to peroxidase	Roche	Cat#11814150001; RRID: AB_390910
Monoclonal ANTI-FLAG® M2 antibody	Sigma-Aldrich	Cat#F1804; RRID: AB_262044
Mouse anti-Influenza A virus nucleoprotein monoclonal antibody (clone AA5H)	Abcam	Cat#ab20343; RRID: AB_445525
Peroxidase-AffiniPure goat anti-mouse IgG (H + L) antibody	Jackson ImmunoResearch	Cat#115-035-003; RRID: AB_10015289
Peroxidase-AffiniPure goat anti-rabbit IgG (H+L) antibody	Jackson ImmunoResearch	Cat#111-035-003; RRID:AB_2313567
Peroxidase-AffiniPure goat anti-mouse IgG, light chain specific antibody	Jackson ImmunoResearch	Cat#115-035-174; RRID: AB_2338512
Peroxidase IgG fraction monoclonal mouse anti-rabbit IgG, light chain specific	Jackson ImmunoResearch	Cat#211-032-171
HA-Tag (6E2) mouse mAb (Alexa Fluor 488 conjugate)	Cell Signaling Technology	Cat#2350
Bacterial and Virus Strains
Influenza A/PR/8/34 (H1N1)	Charles River Laboratories	Cat#10100374
Chemicals, Peptides, and Recombinant Proteins
DiZPK	(Zhang et al., 2011)	N/A
AlPK	(Li et al., 2013a)	N/A
2’-aTCOK	(Peng and Hang, 2016)	N/A
BODIPY-Tz	(Peng and Hang, 2016)	N/A
Bafilomycin A1	Abcam	Cat#ab120497
Cycloheximide (CHX)	Cell Signaling Technology	Cat#2112
MG-132	Selleck	Cat#S2619
Chloroquine (CQ)	Selleck	Cat#S4157
ML240	Sigma-Aldrich	Cat#SML1071
Benzonase	Sigma-Aldrich	Cat#E1014
Protease Inhibitor Cocktail	Roche	Cat#11873580001
DiD	ThermoFisher Scientific	Cat#V22887
12C6-L-lysine	Sigma-Aldrich	Cat#L8662
12C6-L-arginine	Sigma-Aldrich	Cat#A6969
13C6,15N2-L-lysine	Cambridge Isotope	Cat#CNLM-291-H-PK
13C6,15N4-L-arginine	Cambridge Isotope	Cat#CNLM-539-H-PK
DMEM	ThermoFisher Scientific	Cat#11995065
DMEM for SILAC	ThermoFisher Scientific	Cat#88364
Fetal Bovine Serum (FBS)	ThermoFisher Scientific	Cat#26140079
Fetal Bovine Serum (FBS), dialyzed	ThermoFisher Scientific	Cat#26400044
Opti-MEM	ThermoFisher Scientific	Cat#31985070
FluoroBrite DMEM	ThermoFisher Scientific	Cat#A1896701
ProLong Gold Antifade Mountant with DAPI	ThermoFisher Scientific	Cat#P36935
ViaFect Transfection Reagent	Promega	Cat#E4983
Lipofectamine 3000	ThermoFisher Scientific	Cat#L3000015
Xtremegene 9	Roche	Cat#6365809001
DharmaFECT Transfection Reagent	Dharmacon	Cat#T-2001-03
Clarity Western ECL Substrate	Bio-Rad	Cat#1705060
Amersham ECL Select Reagent	GE Healthcare	Cat#RPN2235
Critical Commercial Assays
AlexaFluor-647 Antibody Labeling Kit	ThermoFisher Scientific	Cat#A20186
BCA assay	ThermoFisher Scientific	Cat#23228
QuikChange II Site-Directed Mutagenesis Kit	Agilent Technologies	Cat#200523
Deposited Data
Proteomics database search results	This study; Mendeley Data	https://doi.org/10.17632/tds8by96gc.1
Experimental Models: Cell Lines
HEK293T	ATCC	Cat#CRL-11268
HeLa	ATCC	Cat#CCL-2
IFITM2/3 KO Hela cells	(Spence et al., 2019)	N/A
Oligonucleotides
Control siRNA (CGTACGCGGAATACTTCGA)	(Kirchner et al., 2013)	N/A
VCP siRNA (AACAGCCAUUCUCAAACAGAATT)	(Kirchner et al., 2013)	N/A
UBXD1 siRNA (CCAGGUGAGAAAGGAACUUTT)	(Kirchner et al., 2013)	N/A
Primers for cloning and mutagenesis; See Table S2	This study	N/A
Recombinant DNA
pCMV-DiZPK-PylRS	(Zhang et al., 2011)	Addgene Plasmid #91706
LAMP1-mCherry	(Van Engelenburg and Palmer, 2010)	Addgene Plasmid #45147
Human VCP cDNA	Open Biosystems	Clone #7415
Human IFITM3 cDNA	Open Biosystems	Clone #10410
pCMV-HA vector	TaKaRa	Cat#635690
pCMV-myc vector	TaKaRa	Cat#635689
pCMV-Tag2B vector	Agilent Technologies	Cat#211172
pCMV-HA-IFITM3; See Table S2	This study	N/A
pCMV-HA-IFITM3-TAG mutants; See Table S2	This study	N/A
pCMV-myc-VCP; See Table S2	This study	N/A
pCMV-FLAG-VCP; See Table S2	This study	N/A
Software and Algorithms
ImageLab	Bio-Rad	http://www.bio-rad.com/en-us/product/image-lab-software?ID=KRE6P5E8Z
Graphpad Prism 8	Graphpad	https://www.graphpad.com/
ZEN blue 2012	Zeiss	https://www.zeiss.com/microscopy/int/products/microscope-software/zen.html
Volocity	PerkinElmer	https://www.perkinelmer.com/category/image-analysis-software
FlowJo	FlowJo, LLC	https://www.flowjo.com/
MaxQuant v1.6.3.4	Max Planck Institute of Biochemistry	https://www.maxquant.org/maxquant/
Andromeda	Max Planck Institute of Biochemistry	http://coxdocs.org/doku.php?id=maxquant:andromeda:start
Perseus	Max Planck Institute of Biochemistry	https://www.maxquant.org/perseus/
Other
EZview™ Red anti-HA affinity gels	Sigma-Aldrich	Cat#E6779
EZview™ Red anti-Flag affinity gels	Sigma-Aldrich	Cat#F2426
Pierce™ anti-HA magnetic beads	ThermoFisher Scientific	Cat#88836