|
Antibodies
|
| FLAG M2 |
Sigma |
F1804 (RRID: AB_262044) |
| FLAG M2-HRP |
Sigma |
A8592 (RRID: AB_439702) |
| CHST10 |
Sigma |
PA5-92187 (RRID: AB_2806403) |
| SEL1L |
Sigma |
PA5-88333 (RRID: AB_2804837) |
| DERL1 |
Abcam |
ab176732 (RRID: AB_2858187) |
| BAG6 |
Gift from R.S. Hegde |
N/A |
| TRAPα |
Gift from R.S. Hegde |
N/A |
| TOM20 |
Abcam |
ab186735 (RRID: AB_2889972) |
| ATP13A1 |
Proteintech |
16244-1-AP (RRID: AB_2290293) |
| CNX |
Enzo Life Sciences |
ADI-SPA-865 (RRID: AB_10618434) |
| EMC2 |
Proteintech |
25443-1-AP (RRID: AB_2750836) |
| EMC6 |
Abcam |
Ab84902 (RRID: AB_1925516) |
| GET1 |
Synaptic Systems |
324 002 (RRID: AB_2620063) |
| Ubiquitin |
Santa Cruz Biotechnology |
sc-8017 (RRID: AB_628423) |
| SQLE |
Proteintech |
12544-1-AP (RRID: AB_2195888) |
| OMP25 |
Proteintech |
15666-1-AP (RRID: AB_2201149) |
| PLAT3 |
Abcam |
Ab88447 (RRID: AB_2041691) |
| SPP |
Abcam |
Ab247061 |
| AMFR |
Novus Biologicals |
NBP2-15374 |
| SYVN1 |
Abcam |
Ab170901 (RRID: AB_2833021) |
| RNF185 |
Abcam |
Ab181999 |
| PEX14 |
Proteintech |
10594-1-AP (RRID: AB_2252194) |
| SGTA |
Mateja et al., 2015
|
|
| β-catenin |
Cell Signaling Technology |
9562 (RRID: AB_331149) |
| WNT1 |
Invitrogen |
PIMA515544 |
| FITC-conjugated FLAG M2 |
Sigma |
F4049 (RRID: AB_439701) |
| Peroxidase-conjugated anti-HA antibody |
Cell Signaling Technology |
2999 (RRID: AB_1264166) |
| Peroxidase-conjugated Goat Anti-Mouse |
Jackson ImmunoResearch |
115-035-003 (RRID: AB_10015289) |
| Peroxidase-conjugated Goat Anti-Rabbit |
Jackson ImmunoResearch |
111-035-003 (RRID: AB_2313567) |
| Alexa Fluor 488-conjugated Goat Anti-Mouse |
Jackson ImmunoResearch |
115-545-003 (RRID: AB_2338840) |
| Alexa Fluor 594-conjugated Goat Anti-Rabbit |
Jackson ImmunoResearch |
111-585-003 (RRID: AB_2338059) |
|
Bacterial and virus strains
|
| DH5α E. coli
|
Homemade |
N/A |
|
Biological samples
|
|
|
| RRL-based in vitro translation system |
Feng and Shao, 2018
|
N/A |
| In vitro transcription system |
Feng and Shao, 2018
|
N/A |
|
Chemicals, peptides, and recombinant proteins
|
| Acetonitrile |
Millipore Sigma |
34851 |
| Doxycycline hyclate |
Sigma |
D9891 |
| Hygromycin B |
Millipore Sigma |
31282-04-9 |
| Blasticidin S HCl |
Gibco |
A11139-03 |
| Puromycin |
Gibco |
A11138-03 |
| Bortezomib |
LC laboratories |
B-1408 |
| Epoxomicin |
ApexBio |
134381-21-8 |
| (Z-LL)2-ketone |
Millipore Sigma |
313664-40-3 |
| E1 inhibitor (MLN7243) |
Cayman Chemical |
1450833-55-2 |
| P97 inhibitor (CB-5083) |
Cayman Chemical |
1542705-92-9 |
| Cycloheximide |
Sigma |
01810 |
| Paraformaldehyde |
Electron Microscopy Sciences |
100503-917 |
| MitoTracker CMXRos |
Invitrogen |
M7512 |
| RNase-free DNase |
QIAGEN |
79254 |
| Lys-C protease, MS grade |
ThermoFisher Scientific |
90051 |
| Trypsin Gold, MS grade |
Promega |
V5280 |
| Urea |
Millipore Sigma |
51456 |
| Hydroxylamine, 50% |
ThermoFisher Scientific |
90115 |
| Trifluoroacetic acid, LC-MS grade |
ThermoFisher Scientific |
85183 |
| Formic acid |
Sigma |
27001 |
| cOmplete EDTA-free protease inhibitor cocktail |
Roche |
05056489001 |
| CaptivA PriMAB Protein A affinity resin |
Repligen |
CA-PRI-1000 |
|
Commercial assays
|
| Pierce BCA protein assay kit |
ThermoFisher Scientific |
23225 |
| Pierce quantitative colorimetric peptide assay |
ThermoFisher Scientific |
23275 |
| TMTpro 18-plex label reagent set |
ThermoFisher Scientific |
A52045 |
|
Deposited data
|
| Proteomics data |
MassIVE repository |
MSV000088575 |
|
Experimental models: Cell lines
|
| HEK293T |
ATCC |
CRL-3216 (RRID: CVCL_0063) |
| Flp-In 293 T-REx |
Invitrogen |
R78007 (RRID: CVCL_U427) |
| Flp-In HeLa T-REx |
Gift from B. Raught |
N/A |
| ATP13A1 KO Flp-In HeLa T-REx |
McKenna, Sim et al. 2020
|
N/A |
| ATP13A1 KO Flp-In 293 T-REx |
McKenna, Sim et al. 2020
|
N/A |
| ATP13A1 KO Flp-In 293 T-REx: WT ATP13A1 |
McKenna, Sim et al. 2020
|
N/A |
| ATP13A1 KO Flp-In 293 T-REx HEK293: D533A ATP13A1 |
McKenna, Sim et al. 2020
|
N/A |
| ATP13A1 KO, EMC6 KO Flp-In 293 T-REx |
This study |
N/A |
| Flp-In HeLa T-REx: F-OMP25 |
McKenna, Sim et al. 2020
|
N/A |
| ATP13A1 KO Flp-In HeLa T-REx: F-OMP25 |
McKenna, Sim et al. 2020
|
N/A |
| Flp-In HeLa T-REx: F-BAK1 |
McKenna, Sim et al. 2020
|
N/A |
| Flp-In HeLa T-REx: F-CEND1 |
This study |
N/A |
| ATP13A1 KO Flp-In HeLa T-REx: F-CEND1 |
This study |
N/A |
| GFP(1-10)cyto RFP(1-10)ER Flp-In 293 T-REx |
This study |
N/A |
| GFP(1-10)cyto RFP(1-10)ER ATP13A1 KO Flp-In 293 T-REx |
This study |
N/A |
| GFP(1-10)cyto RFP(1-10)ER Flp-In 293 T-REx: ASGR1-NCb11-P2A-BFP |
This study |
N/A |
| GFP(1-10)cyto RFP(1-10)ER ATP13A1 KO Flp-In 293 T-REx: ASGR1-NCb11-P2A-BFP |
This study |
N/A |
| GFP(1-10)cyto RFP(1-10)ER Flp-In 293 T-REx: DHFR-NCb11-P2A-BFP |
This study |
N/A |
| GFP(1-10)cyto RFP(1-10)ER Flp-In 293 T-REx: BFP-P2A-CNb11-SEC61β |
This study |
N/A |
| GFP(1-10)cyto RFP(1-10)ER Flp-In 293 T-REx: CHST10-NCb11-P2A-BFP |
This study |
N/A |
| GFP(1-10)cyto RFP(1-10)ER ATP13A1 KO Flp-In 293 T-REx: CHST10-NCb11-P2A-BFP |
This study |
N/A |
| GFP(1-10)cyto RFP(1-10)ER Flp-In 293 T-REx: QQ-CHST10-NCb11-P2A-BFP |
This study |
N/A |
| GFP(1-10)cyto RFP(1-10)ER Flp-In 293 T-REx: RR-CHST10-NCb11-P2A-BFP |
This study |
N/A |
| GFP(1-10)cyto RFP(1-10)ER Flp-In 293 T-REx: WNT1-NCb11-P2A-BFP |
This study |
N/A |
| GFP(1-10)cyto RFP(1-10)ER ATP13A1 KO Flp-In 293 T-REx: WNT1-NCb11-P2A-BFP |
This study |
N/A |
| GFP(1-10)cyto RFP(1-10)ER Flp-In 293 T-REx: EGL-20-NCb11-P2A-BFP |
This study |
N/A |
| GFP(1-10)cyto RFP(1-10)ER ATP13A1 KO Flp-In 293 T-REx: EGL-20-NCb11-P2A-BFP |
This study |
N/A |
| GFP(1-10)cyto RFP(1-10)ER Flp-In 293 T-REx: EGL-20H-NCb11-P2A-BFP |
This study |
N/A |
| GFP(1-10)cyto RFP(1-10)ER ATP13A1 KO Flp-In 293 T-REx: EGL-20H-NCb11-P2A-BFP |
This study |
N/A |
| GFP(1-10)cyto RFP(1-10)ER Flp-In 293 T-REx: PRL-NCb11-P2A-BFP |
This study |
N/A |
| GFP(1-10)cyto RFP(1-10)ER ATP13A1 KO Flp-In 293 T-REx: PRL-NCb11-P2A-BFP |
This study |
N/A |
|
Oligonucleotides
|
| SRP14 fwd |
GAGAGCGAGCAGTTCCTGAC |
| SRP14 rev |
GTTTGGTTCGACCGTCATACT |
| TRC8 fwd |
CAAAGCCGGTTCTGCATCG |
| TRC8 rev |
AGTTGCAGCTAACAGAAAGGC |
| MARCH6 fwd |
GTTCCCTTGGATCAGACTCC |
| MARCH6 rev |
CAATGTTCCGGATGCCATTTG |
| EMC6 sg1 fwd |
CACCGGCCGCCTCGCTGATGAACGG |
| EMC6 sg1 rev |
AAACCCGTTCATCAGCGAGGCGGCc |
|
Recombinant DNA
|
| pHDM-G |
PlasmID |
EvNO00061606 |
| pHDM-HGPM2 |
PlasmID |
EvNO00061607 |
| pHDM-tat1B |
PlasmID |
EvNO00061608 |
| pRC-CMV-rev1B |
PlasmID |
EvNO00061616 |
| pHAGE-FLAG-mNG3K(1-10)-P2A-Prl(SS)-mCh3V(1-10)-KDEL |
This study |
N/A |
| pX459 |
Addgene |
62988 |
| pcDNA5 FRT/TO F-OMP25 |
McKenna, Sim et al. 2020
|
N/A |
| pcDNA5 FRT/TO F-CEND1 |
This study |
N/A |
| pcDNA5 FRT/TO GFP-OMP25 |
This study |
N/A |
| pcDNA5 FRT/TO GFP-MAVS |
This study |
N/A |
| pcDNA5 FRT/TO ASGR1-NCb11-P2A-BFP |
This study |
N/A |
| pcDNA5 FRT/TO DHFR-NCb11-P2A-BFP |
This study |
N/A |
| pcDNA5 FRT/TO BFP-P2A-NCb11-SEC61β |
This study |
N/A |
| pcDNA5 FRT/TO CHST10-NCb11-P2A-BFP |
This study |
N/A |
| pcDNA5 FRT/TO QQ-CHST10-NCb11-P2A-BFP |
This study |
N/A |
| pcDNA5 FRT/TO RR-CHST10-NCb11-P2A-BFP |
This study |
N/A |
| pcDNA5 FRT/TO WNT1-NCb11-P2A-BFP |
This study |
N/A |
| pcDNA5 FRT/TO EGL-20-NCb11-P2A-BFP |
This study |
N/A |
| pcDNA5 FRT/TO EGL-20H-NCb11-P2A-BFP |
This study |
N/A |
| pcDNA5 FRT/TO PRL-NCb11-P2A-BFP |
This study |
N/A |
| pSP64 F-OMP25 |
McKenna, Sim et al. 2020
|
N/A |
| pSP64 F-SQS |
This study |
N/A |
| pSP64 F-STX1B |
This study |
N/A |
| pSP64 CHST10-FLAG |
This study |
N/A |
| pSP64 RR-CHST10-FLAG |
This study |
N/A |
| pSP64 EGL-20-FLAG |
This study |
N/A |
| pSP64 EGL-20H-FLAG |
This study |
N/A |
| pSP64 PRL-FLAG |
This study |
N/A |
| pDONR ASGR1 |
DNASU |
HsCD00005525 |
| pDONR CHST10 |
Gift from the Harper lab |
N/A |
| pRK5-HA-ubiquitin-WT |
Addgene |
17608 |
| pTAG-BiP(SS)-BFP-KDEL |
Friedman et al., 2011
|
N/A |
|
Software and algorithms
|
| ImageJ |
NIH |
N/A |
| Prism 9 |
GraphPad |
N/A |
| FlowJo v10 |
FlowJo |
N/A |
| Illustrator |
Adobe |
N/A |
| Photoshop |
Adobe |
N/A |
| ImageQuant TL |
Cytiva |
N/A |
| In-house MS data analysis software |
Huttlin et al., 2010
|
N/A |
|
Other
|
| Control siRNA |
Horizon |
D-001810-10-05 |
| EMC2 siRNA |
Horizon |
L-010631-00-0005 |
| EMC5 siRNA |
Horizon |
L-018365-00-0005 |
| EMC6 siRNA |
Horizon |
L-014711-02-0005 |
| WRB siRNA |
Horizon |
L-011898-01-0005 |
| ATP13A1 siRNA |
Horizon |
L-020426-00-0005 |
| SPP siRNA |
Horizon |
L-005896-00-0005 |
| TRC8 siRNA |
Horizon |
L-006942-00-0005 |
| MARCH6 siRNA |
Horizon |
L-006925-00-0005 |
| AMFR siRNA |
Horizon |
L-006522-00-0005 |
| SYVN1 siRNA |
Horizon |
L-007090-00-0005 |
| RNF185 siRNA |
Horizon |
L-007107-00-0005 |
| SEL1L siRNA |
Horizon |
L-004885-00-0005 |
| BAG6 siRNA |
Horizon |
L-005062-01-0005 |
| DERL1 siRNA |
Horizon |
L-010733-02-0005 |
| DMEM + GlutaMAX |
Gibco |
10569-010 |
| FluoroBrite DMEM |
Gibco |
A1896701 |
| Trypsin-EDTA |
Gibco |
25200-056 |
| PBS |
Gibco |
10010-023 |
| DMSO |
Sigma |
472301 |
| OPTI-MEM |
Gibco |
31985-062 |
| TransIT-293 |
Mirus |
MIR 2706 |
| Lipofectamine 3000 |
Invitrogen |
L3000-015 |
| Lipofectamine RNAiMAX |
Invitrogen |
13778-150 |
| SuperSignal West Pico PLUS Chemiluminescent Substrate |
ThermoFisher Scientific |
34580 |
| Ponceau S solution |
Sigma |
P7170 |
| EasyTag L-[35S]-Methionine |
Perkin Elmer |
NEG709A005MC |
| Polypropylene Microfuge Tubes |
Beckman Coulter |
357448 |
| Digitonin |
Millipore Sigma |
11024-24-1 |
| Triton X-100 |
Sigma |
T9284 |
| Tween 20 |
Sigma |
P7949 |
| 10% SDS |
Sigma |
71736 |
| 40% acrylamide (29:1) |
Bio Rad |
1610146 |
| Nitrocellulose membrane |
Bio Rad |
1620112 |
| Multi-well glass-bottom cell culture plates |
MatTek |
P24G-1.5-13-F |
| BioMax MR film |
Carestream |
894 1114 |
| Buffer RLT |
QIAGEN |
79216 |
| RNeasy Mini Kit |
QIAGEN |
74106 |
| SuperScript III First-Strand Synthesis System |
Invitrogen |
18080051 |
| SYBR Green Master Mix |
Applied Biosystems |
4309155 |
| Pierce C18 tips, 100 μL |
ThermoFisher Scientific |
87784 |
| Sep-Pak C18 cartridge, 100 mg |
Waters |
Wat036935 |
| 300Extend C18 column |
Agilent |
custom |
| Accucore 150 resin |
ThermoFisher Scientific |
16126-000 |
