KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-HA Peroxidase High Affinity (3F10, rat) | Roche | 12013819001 |
| Anti-HA (12CA5, mouse) | Roche | 11583816001 |
| Anti-glucose-6-phosphate-dehydrogenase (Rabbit) | Sigma-Aldrich | A9521 |
| Anti-GFP (3E6, mouse) | Invitrogen | A-11120 |
| Anti-GFP (mouse) | Roche | 11814460001 |
| Anti-Ubiquitin (P4D1, mouse) | Santa Cruz Biotechnology | SC-8017 |
| Anti-FLAG (DYKDDDDK tag antibody 2368, rabbit) | Cell Signaling Technology | 2368S |
| Anti-rabbit IgG, HRP-linked antibody (Goat) | Cell Signaling Technology | 7074S |
| Anti-mouse IgG, HRP-linked antibody (Horse) | Cell Signaling Technology | 7076S |
| Anti-Ydj1 (Rabbit) | Avrom Caplan Lab | Caplan and Douglas, 1991 |
| Anti-Erv46 (Rabbit) | Charles Barlowe Lab | N/A |
| Anti-Sec61 (Rabbit) | This Lab | N/A |
| Anti-Ubx2 (Rabbit) | Thomas Becker Lab | N/A |
| Bacterial and virus strains | ||
| CBB205 | Sar1-GST | Barlowe et al., 1994 |
| E.coli (BL21) | NEB | C2530H |
| Chemicals, peptides, and recombinant proteins | ||
| ProSignal Pco ECL Reagent | Genesee Scientific | 20-300B |
| ProSignal Femto ECL Reagent | Genesee Scientific | 20-302B |
| Cycloheximide | Sigma-Aldrich | C7698 |
| Oligomycin | Sigma-Aldrich | O4876-5MG |
| MG132 | Millipore | 474790 |
| GTP | Sigma-Aldrich | G8877 |
| ATP | Sigma-Aldrich | A2383 |
| Creatine phosphate | Roche | 10621722001 |
| Creatine Phosphokinase | Sigma-Aldrich | C3755 |
| Phenylmethanesulfonyl fluoride (PMSF) | Sigma-Aldrich | P7626 |
| Leupeptin | Sigma-Aldrich | L9783 |
| Pepstatin A | Sigma-Aldrich | P5318 |
| N-ethylmaleimide (NEM) | Sigma-Aldrich | E1271 |
| Thrombin from human plasma | Sigma-Aldrich | T6884 |
| Isopropyl β-D-thiogalactoside (IPTG) | Sigma-Aldrich | 16758 |
| CellTracker Blue CMAC Dye | Invitrogen | C2110 |
| 4’,6’-Diamidino-2-phenylinadole (DAPI) | Sigma-Aldrich | D8417 |
| Triton X-100 | Sigma-Aldrich | X100 |
| Dodecyl-beta-D-maltoside (DDM) | Calbiochem | D310 |
| Critical commercial assays | ||
| Pierce BCA Protein Assay Kit | Thermo Fisher | 23225 |
| EasyTag EXPRESS 35S Protein Labeling Mix | PerkinElmer Life Sciences | NEG772014MC |
| Deposited data | ||
| Raw data files | This study | N/A |
| Experimental models: Organisms/strains | ||
| BY4742 | MATα, his3Δ1, leu2Δ0, lys2Δ0 ura3Δ3 | Winzeler et al., 1999 |
| pdr5Δ | MATα, his3Δ1, leu2Δ0, ura3Δ3 pdr5Δ::KanMX | Winzeler et al., 1999 |
| pdr5Δpep4Δ | MATα, met15Δ0, his3Δ1, leu2Δ0, ura3Δ3 pdr5Δ::KanMX, pep4Δ::KanMX | Winzeler et al., 1999 |
| ydj1Δ | MATα, his3Δ1, leu2Δ0, ura3Δ3 ydj1Δ::KanMX | Winzeler et al., 1999 |
| vps36Δ | MATα, his3Δ1, leu2Δ0, ura3Δ3 vps36Δ::KanMX | Winzeler et al., 1999 |
| hrd1Δ | MATα, his3Δ1, leu2Δ0, ura3Δ3 hrd1Δ::KanMX | Winzeler et al., 1999 |
| doa10Δ | MATα, his3Δ1, leu2Δ0, ura3Δ3 doa10Δ::KanMX | Winzeler et al., 1999 |
| ubx1Δ | MATα, his3Δ1, leu2Δ0, ura3Δ3 ubx1Δ::KanMX | Winzeler et al., 1999 |
| ubx2Δ | MATα, his3Δ1, leu2Δ0, ura3Δ3 ubx2Δ::KanMX | Winzeler et al., 1999 |
| ubx4Δ | MATα, his3Δ1, leu2Δ0, ura3Δ3 ubx4Δ::KanMX | Winzeler et al., 1999 |
| cuelΔ | MATα, his3Δ1, leu2Δ0, ura3Δ3 cue1Δ::KanMX | Winzeler et al., 1999 |
| npl4Δ | MATα, his3Δ1, leu2Δ0, ura3Δ3 npl4Δ::KanMX | Winzeler et al., 1999 |
| rad23Δ | MATα, his3Δ1, leu2Δ0, ura3Δ3 rad23Δ::KanMX | Winzeler et al., 1999 |
| dsk2Δ | MATα, his3Δ1, leu2Δ0, ura3Δ3 dsk2Δ::KanMX | Winzeler et al., 1999 |
| cdc48-2 | Backcrossed 3X to BY4742 | Moir et al., 1982 |
| ySZ083 | UBX2-3FLAG::HIS BY4742 | This study |
| ySZ084 | doa10Δ::KanMX UBX2-3FLAG::HIS BY4742 | This study |
| ySZ087 | ubx2Δ::KanMX PUBX2-UBX2::LEU BY4742 | This study |
| ySZ088 | ubx2Δ::KanMX PUBX2-UBX2(ΔUBA)::LEU BY4742 | This study |
| ySZ089 | ubx2Δ::KanMX PUBX2-UBX2(ΔUBX)::LEU BY4742 | This study |
| ySZ090 | ubx2Δ::KanMX PUBX2-UBX2(ΔUBA ΔUBX)::LEU BY4742 | This study |
| Sec13-RFP | Allison O’Donnell lab | |
| CBY120 | Sec13/Sec31 purification | Charles Barlowe lab |
| CBY1285 | Sec23/Sec24 purification | Charles Barlowe lab |
| sec12-4 | MATa, SUC2, mal mel gal2 CUP1, sec12-4 | Novick et al., 1980 |
| Oligonucleotides | ||
| OSZ08 | GTACTCTAGAATGTTTTTCAACAGACTAAG | Sun and Brodsky, 2018 |
| OSZ14 | GCCTTTAGACATGGAGCCTGAGCCACCTCCT | This study |
| OSZ15 | AGGAGGTGGCTCAGGCTCCATGTCTAAAGGC | This study |
| OSZ16 | GTCAGGATCCCTTTGTACAATTCGTCCATTC | This study |
| RE113 | GCACTGGATGAAGAAGATGAAGAAGATGAGGAAAATGAAGAACAAGGGGGAGGCGGGGGTGGA | Surma et al., 2013 |
| RE114 | CTCTTTGTACGCGTTTGTCGTTTTTAACGATATGCTATTTTAGAATTCGAGCTCGTTTAAAC | Surma et al., 2013 |
| OSZ17 | AGCTTCCTCACTTGGATTCTTAGCTGCTTGGTATTTTAAGGCGCATTTTC | This study |
| OSZ18 | GAAAATGCGCCTTAAAATACCAAGCAGCTAAGAATCCAAGTGAGGAAGCT | This study |
| OSZ21 | GTCATCTAGAACTAGTATGAAAGCATTCACCAGT | This study |
| OSZ22 | GTCAGGATCCCAGCTTTGTACAATTCGTCCAT | This study |
| oSZ23 | GCTTTGTACAATTCGTCCATTCCGCGGCCGCGTTTGTATAGTTCAT | This study |
| OSZ24 | GAACTTAGTTTCGACGGATT | This study |
| OSZ25 | ATGAACTATACAAACGCGGCCGCGGAATGGACGAATTGTACAAAGC | This study |
| OSZ26 | GTGACATAACTAATTACATGACTCGAGTTAGCGGCCGCAAGCTTGCATGCCGGTAGAGGTGTG | This study |
| Recombinant DNA | ||
| pSZ01 | CEN URA3 P-TEF SZ* | Sun and Brodsky, 2018 |
| pSZ03 | CEN URA3 P-TEF SZ*-GFP | Sun and Brodsky, 2018 |
| pSW148 | CEN LEU2 P-GAS Wsc1* | Wang and Ng, 2010 |
| pSW144 | CEN LEU2 P-PRC1 ED-Wsc1-L63R | Wang and Ng, 2010 |
| BPM390 | CEN LEU2 P-YDJ1 Ydj1 | Elizabeth Craig lab |
| pTY40 | Sar1-GST | Barlowe et al., 1994 |
| pSZ10 | CEN URA3 P-TEF SZ*-GFP-Ub4 | This study |
| pSZ11 | CEN LEU2 P-YDJ1 Ydj1 (HPD/QAA) | This study |
| pSZ12 | CEN URA3 P-TEF SZ*-GFP-Ub4* | This study |
| pSZ13 | CEN LEU2 P-TEF SZ*-GFP | This study |
| pRS315 | CEN LEU2 | ATCC |
| pKN31 | 2μ HIS3 Pcup1-mycUb-Tcyc1 | Nakatsukasa et al., 2008 |
| pSZ14 | CEN URA3 P-TEF ED-Ub4 | This study |
| pSZ15 | CEN LEU2 P-GPD Yor1-GFP-Ub4 | This study |
| pSZ16 | CEN LEU2 P-GPD Pca1(1-392)-Yor1-GFP-Ub4 | This study |
| pFA6a-6xGly-3xFLAG-HIS3MX6 | 6xGly-3xFLAG-HIS3MX6 | Lee et al., 2013 |
| 4625 | LEU2 Pubx2 Ubx2(1-585)-Cyc1term | Wang and Lee, 2012 |
| 4628 | LEU2 Pubx2 Ubx2(71-585)-Cyc1term | Wang and Lee, 2012 |
| 4626 | LEU2 Pubx2 Ubx2(1-410)-Cyc1term | Wang and Lee, 2012 |
| 4623 | LEU2 Pubx2 Ubx2(71-410)-Cyc1term | Wang and Lee, 2012 |
| SFNB2443 | LEU2 pRS305-SEC24-2xmCherry | Susan Ferro-Novick Lab |
| 105 | CEN LEU2 PGPD-Yor1-GFP | Adle et al., 2009 |
| 106 | CEN LEU2 PGPD-Pca1(1-392)-Yor1-GFP | Adle et al., 2009 |
| 1677 | CEN LEU2 Ppol30 Pol30-Ub-Ub-Ub-Ub | Zhao and Ulrich, 2010 |
| Software and algorithms | ||
| ImageJ 1.48V | NIH | https://imagej.net/ |
| FIJI (2.0.0-rc-69/1.52i) | NIH | https://imagej.net/software/fiji |
| GraphPad Prism (7.0c) | GraphPad Software | https://www.graphpad.com/ |
| Other | ||
| Anti-HA Affinity Matrix | Roche | 11815016001 |
| Protein A-Sepharose CL-4B | GE Healthcare | GE17-0780-01 |
| DEAE Sepharose Fast Flow | GE Healthcare | 17070910 |
| Q Sepharose XL | GE Healthcare | 10252711 |
| Ni-NTA agarose | QIAGEN | 30230 |
| Glutathione-Agarose | Millipore | G4510 |
| Amicon Ultra-15 Centrifugal Filter Unit | Millipore | UFC903024 |