REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse anti-HA mAb	Sigma-Aldrich	Cat#: H9658; RRID: AB_260092
Rabbit anti-HA pAb	Proteintech	Cat#: 51064-2-AP; RRID: AB_11042321
Mouse anti-FLAG® M2 mAb	Sigma-Aldrich	Cat#: F1804; RRID: AB_262044
Rabbit anti-Flag mAb	Abclonal	Cat#: AE092
Mouse anti-Myc mAb	Cell Signaling Technology	Cat#: 2276; RRID: AB_331783
Mouse anti-β-actin	Sigma-Aldrich	Cat#: A5441; RRID: AB_476744
Mouse anti-Strep-tag II [GT661]	Abcam	Cat#: ab184224
Mouse anti-SQSTM1 (clone: 2C11)	Abnova	Cat#: H00008878-M01; RRID: AB_437085
Mouse anti-CHOP (L63F7)	Cell Signaling Technology	Cat#: 2895; RRID: AB_2089254
Rabbit anti-Atg7 mAb	Cell Signaling Technology	Cat#: 8558; RRID: AB_10831194
Mouse anti-mCherry mAb	Abclonal	Cat#: AE002; RRID: AB_2770407
Mouse anti-GFP mAb	Abclonal	Cat#: AE012; RRID: AB_2770402
Mouse anti-GST mAb	Abclonal	Cat#: AE001; RRID: AB_2770403
Mouse anti-MBP mAb	Abclonal	Cat#: AE016; RRID: AB_2770406
Mouse anti-His mAb	Abclonal	Cat#: AE003; RRID: AB_2728734
Mouse anti-double stranded RNA (J2)	Scicons	Cat#: 10010200; RRID: AB_2651015
Rabbit anti-SERP1 (RAMP4) pAb	Proteintech	Cat#: 17807-1-AP; RRID: AB_10597394
Rabbit anti-REEP5 pAb	Proteintech	Cat#: 14643-1-AP; RRID: AB_2178440
Rabbit anti-FAM134B pAb	Proteintech	Cat#: 21537-1-AP; RRID: AB_2878879
Rabbit anti-CKAP4 (CLIMP63)	Proteintech	Cat#: 16686-1-AP; RRID: AB_2276275
HRP-conjugated Goat Anti-Mouse IgG (H+L)	Abclonal	Cat#: AS003; RRID: AB_2769851
HRP-conjugated Goat Anti- Rabbit IgG (H+L)	Abclonal	Cat#: AS014; RRID: AB_2769854
HRP-conjugated Goat Anti-Mouse IgG Heavy Chain	Abclonal	Cat#: AS064; RRID: AB_2864058
HRP-conjugated AffiniPure Goat Anti-Mouse IgG Light Chain	Abclonal	Cat#: AS062; RRID: AB_2864056
Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488	Thermo Fisher Scientific	Cat#: A32723; RRID: AB_1549585
Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor Plus 488	Thermo Fisher Scientific	Cat#: A32731; RRID: AB_2633280
Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 568	Thermo Fisher Scientific	Cat#: A-11031; RRID: AB_144696
Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 568	Thermo Fisher Scientific	Cat#: A-11036; RRID: AB_10563566
Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647	Thermo Fisher Scientific	Cat#: A-21236; RRID: AB_2535805
Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647	Thermo Fisher Scientific	Cat#: A-21244; RRID: AB_2535812
Bacterial and virus strains
E. coli DH5α (DE3)	This paper	N/A
E. coli BL21	This paper	N/A
SARS-CoV-2 (WBP)	This paper	Hubei Provincial Center for Disease Control and Prevention
Chemicals, peptides, and recombinant proteins
1,6-hexanediol	Macklin	Cat#: H810887
Chloroquine	Sigma-Aldrich	Cat#: C6628
DSS	Thermo Fisher Scientific	Cat#: 21655
Cyclopiazonic acid (CPA)	GLPBIO	Cat#: GC10268
Thapsigargin (Tg)	Cell Signaling Technology	Cat#: 12758
Polyethylenimine (PEI)	Yeasen	Cat#: 40815ES03
Lipofectamine 2000 transfection reagent	Invitrogen	Cat#: 11668019
Phosphate buffered saline (PBS)	Hyclone	Cat#:SH30256.01
Dulbecco’s modified eagle’s medium (DMEM)	Gibco	Cat#: 11995065
Fetal bovine serum (FBS)	Sigma-Aldrich	Cat#: 12303C
Penicillin-Streptomycin	Gibco	Cat#: 15140163
0.25% Trypsin-EDTA	Gibco	Cat#: 25200056
OPTI-MEM	Gibco	Cat#: 31985088
Protease inhibitor cocktail	Biosharp	Cat#: BL612A
Earle’s balanced salt solution (EBSS)	Sigma-Aldrich	Cat#: E2888
Anti-Flag M2 affinity gel	Sigma-Aldrich	Cat#: A2220
Anti-HA magnetic beads	Bimake	Cat#: B26202
Streptactin beads 4FF	Smart Lifesciences	Cat#: SA053005
MBPSep Dextrin Agarose Resin 6FF	Yeasen	Cat#: 20515ES08
Glutathione Resin	Genscript	Cat#: L00206
L-Glutathione reduced (GSH)	Biofrox	Cat#: 1392GR005
DAPI	Servicebio	Cat#: G1012-10ML
Paraformaldehyde	Servicebio	Cat#: G1101-500ML
Bovine serum albumin (BSA)	Fisher Scientific	Cat#: BP1600-100
Triton X-100	Solarbio	Cat#: T8200
Critical commercial assays
Pierce BCA Protein Assay Kit	Thermo Fisher Scientific	Cat#: 23225
Experimental models: Cell lines
HEK293T cells	CCTCC (China Center for Type Culture Collection)	Cat#: GDC187
HeLa cells	ATCC	Cat#: CCL-2
Vero E6 cells	Hubei Provincial Center for Disease Control and Prevention, China	N/A
U2OS cells	ATCC	Cat#: HTB-96
Oligonucleotides
siRNA Targeting sequences: p62: GCATTGAAGTTGATATCGAT	This paper	N/A
siRNA Targeting sequences: Atg7 #1: GCCAACAUCCCUGGAUACAAG	This paper	N/A
siRNA Targeting sequences: Atg7 #2: CUGUGAACUUCUCUGACGU	This paper	N/A
shRNA Targeting sequences for FAM134B: GAGGTATCCTGGACT GATAAT	This paper	N/A
sgRNA Targeting sequences for p62: GTGCGCCTGGAAGCCGC	This paper	N/A
Recombinant DNA
pLVX-EF1a-ORF8-Strep	Nevan J. Krogan Lab	Gordon et al., 202021
pEGFP-C1-FAM134B	Qiming Sun Lab	Jiang et al., 202044
pEGFP-C1-FAM134B-Δ84-233	Qiming Sun Lab	Jiang et al., 202044
mCherry-GFP-FAM134B	Qiming Sun Lab	Jiang et al., 202044
pCDNA5-RTN3L-Flag	Qiming Sun Lab	N/A
pGEX-4T-GST-p62	This paper	N/A
pEGFP-C3-p62	Li Yu Lab	Sun et al., 201838
pEGFP-C3-p62-ΔPB1	Li Yu Lab	Sun et al., 201838
pEGFP-C3-p62-S403E	Li Yu Lab	Sun et al., 201838
pEGFP-C3-p62-M404V	Li Yu Lab	Sun et al., 201838
MBP-mCherry-p62	Li Yu Lab	Sun et al., 201838
Flag-p62	Wei Liu Lab	You et al., 201941
Flag-p62-Δ1-85	Wei Liu Lab	You et al., 201941
Flag-p62-Δ86-121	Wei Liu Lab	You et al., 201941
Flag-p62-Δ122-168	Wei Liu Lab	You et al., 201941
Flag-p62-Δ169-253	Wei Liu Lab	You et al., 201941
Flag-p62-Δ254-310	Wei Liu Lab	You et al., 201941
Flag-p62-Δ311-384	Wei Liu Lab	You et al., 201941
Flag-p62-Δ385-440	Wei Liu Lab	You et al., 201941
pCDNA5-CCPG1-Flag	This paper	N/A
pCDNA3.1-scFv-ORF8-VIF-1/-2	Hui Zhang Lab	Zhang et al., 202120
pGEX-4T-GST-GFP-ORF8	This paper	N/A
MBP-ORF8	Yan Li Lab	N/A
pCDNA4-ORF8-Flag	This paper	N/A
pCDNA4-GFP-ORF8	This paper	N/A
pCDNA4-GFP-ORF8-HA	This paper	N/A
pGEX-4T-GST-FAM134B	This paper	N/A
pCDNA4-FAM134B-HA	This paper	N/A
pCDNA4-ATL3-HA	This paper	N/A
pCDNA4-TEX264-HA	This paper	N/A
pCDNA4-SEC62-HA	This paper	N/A
pCDNA4-p62-Flag	This paper	N/A
pCDNA4-p62-Δ250-270-Flag	This paper	N/A
pCDNA4-p62-Δ260-280-Flag	This paper	N/A
pCDNA4-p62-Δ270-290-Flag	This paper	N/A
pCDNA4-p62-Δ280-300-Flag	This paper	N/A
pCDNA4-p62-Δ290-310-Flag	This paper	N/A
pCDNA4-p62-EHGG-AAAA-Flag	This paper	N/A
pCDNA4-p62-KRSR-AAAA-Flag	This paper	N/A
pCDNA4-p62-LTPV-AAAA-Flag	This paper	N/A
pCDNA4-p62-SPES-AAAA-Flag	This paper	N/A
pCDNA4-p62-SSTE-AAAA-Flag	This paper	N/A
mCherry-sec61β	This paper	N/A
pCDNA4-mCherry-RAMP4-HA	This paper	N/A
pCDNA4-mCherry-GFP-RAMP4-HA	This paper	N/A
pCDNA4-M-Flag	This paper	N/A
HA-Ub	This paper	N/A
pCDNA4-p62-HA	This paper	N/A
pEGFP-LC3	This paper	N/A
pCDNA4-Keap-HA	This paper	N/A
pCDNA4-SARS-CoV-ORF8-Flag	This paper	N/A
pCDNA4-MERS-CoV-ORF8-Flag	This paper	N/A
NSP3-Myc	This paper	N/A
NSP4-Myc	This paper	N/A
Software and algorithms
GraphPad Prism 8	GraphPad Software	N/A
Image J	NIH	https://imagej.en.softonic.com/
IUPred2A	N/A	https://iupred2a.elte.hu/