Table of reagents and resources.
| Reagent or resource | Reference or source | Identifier or Cat. no. |
| Affinity beads/agarose | ||
| ANTI-FLAG M2 Affinity Gel | Sigma-Aldrich | A2220-1ML |
| Glutathione Sepharose 4B | GE Healthcare | 17-0756-01 |
| HA peptide | Sigma-Aldrich | I2149-1MG |
| Anti-HA agarose | Sigma-Aldrich | A2095-5X1ML |
| Pierce Anti-HA agarose | Thermo Fisher Scientific | 26182 |
| PTMScan Ubiquitin Remnant Motif (K-ε-GG) Kit | Cell Signaling | 5562 |
| Streptavidin agarose | Sigma-Aldrich | S1638-5ML |
| UM101: TUBE 1 | Lifesensors | UM-0101-1000 |
| Primary Antibodies | ||
| α-tubulin | Abcam | ab7291 |
| Anti-KAP1 antibody | Abcam | ab22553 |
| APEX (IgG2A) | Regina Feederle | Custom made |
| Biotin | Pierce | 31852 |
| Biotin FITC | Abcam | ab6650 |
| Cyclin-F | Santa Cruz | sc-952 |
| DNAJC7 | Proteintech | 11090-1-AP |
| FlaG M2 | Cell signaling | 2368 |
| HA.11 | Covance/BioLegend | MMS-101P/901501 |
| HSF1 | Cell Signaling | 4356 |
| HSP90β | Cell Signaling | 7411 |
| Ub K48 | Cell Signaling | 8081 |
| Nrf2 | Abcam | ab62352 |
| p62/SQSTM1 | BD | 610832 |
| PCNA | Santa Cruz | sc-7907 |
| PCNA (PC10) | Santa Cruz | sc-56 |
| Skp1 | Cell Signaling | 2156 |
| STIP1 | Abcam | ab126724 |
| STUB-1/CHIP | Bethyl Laboratories | A301-572A |
| TBK1/NAK | Abcam | ab40676 |
| Tollip | Abcam | ab187198 |
| Secondary ABs | ||
| Anti-goat-HRP | Promega | V8051, RRID: AB_430838 |
| Anti-mouse-HRP | Promega | W402B |
| Anti-rabbit-HRP | Promega | W401B |
| Anti-rat-HRP | Sigma-Aldrich | A-9037, RRID: AB_258429 |
| Software/Tools | ||
| Adobe Illustrator 2022 | Adobe | |
| Fiji, ImageJ | N/A | Version 1.53j |
| gRNA design Tool | portals.broadinstitute.org/gpp/public/analysis-tools/sgrna-design | |
| gRNA design Tool - CRISPOR | crispor.tefor.net | |
| MaxQuant | N/A | Version 1.6.0.1 |
| Perseus | N/A | Version 1.6.10.43 |
| QuikChange Primer Design | https://www.agilent.com/store/primerDesignProgram.jsp | |
| R | Version 4.1.1 | |
| R-Studio | Version 1.4.1717 | |
| Plasmids/Vectors | ||
| ORF CCNF | Dharmacon | MHS6278-202831979 |
| ORF FBXO28 | Dharmacon | OHS1770-202323126 |
| ORF HSP90AB1 | Horizon Discovery | MHS6278-202807158 |
| pHAGE-N-myc-APEX2 | Zellner et al (2021) (52) | |
| pMD2.G | Addgene | 12259 |
| psPAX2 | Addgene | 12260 |
| pSpCas9(BB)-2A-Puro (PX459) V2.0 | Addgene | 62988 |
| gRNAs/Primers | ||
| sgRNA1_mouse-Seq: CACCGAGACAACACGTATAAATACG | Thermo Fisher Scientific | Custom order |
| sgRNA2_mouse-Seq: CACCGGTAACTGACACTCCGCTCGG | Thermo Fisher Scientific | Custom order |
| sgRNA1_human CCNF- Seq: ACACCGCGTTTGGTTCTCCGCCCCGAG | Thermo Fisher Scientific | Custom order |
| sgRNA2_human_CCNF-Seq: ACACCGGTAGACCACGGTGACATCGG | Thermo Fisher Scientific | Custom order |
| Sequencing primer human CCNF gRNA1_fw TTTGTCCATGTGGTGTGTGT | Thermo Fisher Scientific | Custom order |
| Sequencing primer human CCNF gRNA1 rev TGAGATAGGAGAGGCGGGT | Thermo Fisher Scientific | Custom order |
| Sequencing primer human CCNF gRNA2 fw TTTCCCGGTTGCTTGCTT | Thermo Fisher Scientific | Custom order |
| Sequencing primer human CCNF gRNA2 rev CATGTCCTCCTCCTCACT | Thermo Fisher Scientific | Custom order |
| Sequencing primer mouse CCNF - gRNA2_fw GAGGAAGGTGGAGGATGT | Thermo Fisher Scientific | Custom order |
| Sequencing primer mouse CCNF - gRNA2_rev TCTCCTACAACTACTCCC | Thermo Fisher Scientific | Custom order |
| Sequencing primer mouse CCNF - gRNA1_fw GGGTTATGTAGGGGTCAG | Thermo Fisher Scientific | Custom order |
| Sequencing primer mouse CCNF - gRNA1_rev AGACAAGAGGGAGGAAAA | Thermo Fisher Scientific | Custom order |
| Cell lines | ||
| LCL, ctrl 1, female | Jochen Weishaupt | This study |
| LCL, ctrl 2, female | Jochen Weishaupt | This study |
| LCL, CCNF V335M, female | Jochen Weishaupt | This study |
| LCL, ctrl 3, male | Jochen Weishaupt | This study |
| LCL, ctrl 4, male | Jochen Weishaupt | This study |
| LCL, CCNF D628V, male | Jochen Weishaupt | This study |
| N2a cells | ATCC | CCL-131 |
| SH-SY5Y cells | ATCC | CRL-2266 |
| Kits | ||
| Amaxa SF Cell Line 4D-Nucleofector X Kit | Lonza | V4XC-2012 |
| Pierce BCA Protein Assay Kit | Thermo Fisher Scientific | 23225 |
| PureLink Genomic DNA Kit | Invitrogen | K1820-02 |
| QIAprep Spin Miniprep kit | QIAGEN | 27106 |
| Chemicals/enzymes | ||
| Acrylamide solution | PanReac AppliChem | A0951 |
| Ammonium bicarbonate | Sigma-Aldrich | 9830 |
| BbsI | NEB | R0539S |
| Benzonase | Merck Millipore | 71205-3 |
| Biotin-Phenol | Iris Biotech | LS-3500.5000 |
| Bortezomib 99% | LC Labs | B-1408 |
| BSA | Sigma-Aldrich | A8022-100G |
| Complete | Roche | 4693132001 |
| Disodiumhydrogenphoshpate | Merck | 1.06580.5000 |
| Dithiothreitol | Sigma-Aldrich | 43815-5G |
| Dulbecco’s PBS | Thermo Fisher Scientific | 14190169 |
| Ethylenediaminetetraacetic acid | Merck | 1.008418.1000 |
| Glycerol | Roth | 3783 |
| GO-Taq polymerase | Promega | M784B |
| Hydrogenperoxide | Sigma-Aldrich | H1009 |
| IGEPAL CA-630 (NP-40) | Sigma-Aldrich | I8896 |
| KOD Hot Start DNA Polymerase | Sigma-Aldrich | 71086 |
| Lipofectamine 2000 | Invitrogen | 11668-019 |
| N-Ethylmaleimide (NEM) | Sigma-Aldrich | E3876-5G |
| Opti-MEM | Invitrogen | 31985-062 |
| Paraformaldehyde solution 4% | Chemcruz | sc-281692 |
| Phenylmethylsulfonyl fluoride | Sigma-Aldrich | P7626-1G |
| PhosSTOP | Roche | 4906837001 |
| ProLong Gold Antifade | Invitrogen | P36931 |
| Puromycin dihydrochloride | Sigma-Aldrich | P8833-100mg |
| Pwo-polymerase | VWR | 01-5010-88 |
| Recombinant USP2 | R&D Systems | E-504-050 |
| Sodium L-ascorbate | Sigma-Aldrich | A7631 |
| TCEP | ROTH | HN95.2 |
| Trifluoroacetic acid | Honeywell Fluka | 302031-100ML |
| Triton X-100 | Merck | 1.08603.1000 |
| Trolox | Sigma-Aldrich | 238813 |
| Tropix I-Block | Appliedbiosystems | T2015 |
| Trypsin, sequencing-grade | Promega | V5113 |
| Western Lightning Plus-ECL | PerkinElmer | NEL104001EA |
| X-tremeGENE HP | Roche | 06 366 236 001 |
| Hardware/Consumables | ||
| 4D-NucleofectorTM X Unit | Lonza | |
| Amersham Protran 0.45 μm NC | GE Healthcare Life Science | 10600002 |
| EMPORE Octadecyl C18 47 mm | Supelco Analytical | 66883-U |
| Lyophilisator, Alpha 1-2 LD Plus | CHRIST | N/A |
| Mini-PROTEAN Tetra cell | Bio-Rad | 1658004EDU |
| Mini-Transblot cell | Bio-Rad | 1703930 |
| Sonifier | SONIFIER Branson | W-250D |
| Super RX-N | Fujifilm | 47410 19289 |
| Ultrafree-MC, HV 0.45 μm | Merck Millipore | UFC30HV00 |
| Vacuum Centrifuge | Eppendorf | N/A |
| Zeiss LSM800 oil 60× objective | Zeiss | N/A |
| Easy-NLC1200 | Thermo Fisher Scientific | N/A |
| QExactiveHF mass spectrometer | Thermo Fisher Scientific | N/A |