Table S3.
Mass spectrometry analysis of Ubv interactions in HEK293T cells
| ID* | Gene† | Description | V‡ | Ub‡ | Fw7.5 | Fw7.5 dimer | Fw11.2 | Fw11.2dimer |
| All Ubv | ||||||||
| P63208 | SKP1 | Skp1 | 0§ | 0 | 18 | 37 | 57 | 40 |
| P68363 | TUBA1B | Tubulin | 21 | 12 | 21 | 66 | 36 | 2 |
| Q09028 | RBBP4 | Histone binding | 2 | 0 | 0 | 12 | 0 | 0 |
| P53671 | LIMK2 | Histone kinase | 0 | 0 | 10 | 10 | 8 | 5 |
| Q9H479 | FN3K | Ketosamine-3-kinase | 0 | 0 | 9 | 0 | 4 | 0 |
| O15018 | PDZD2 | PDZ domain containing | 0 | 0 | 2 | 5 | 5 | 1 |
| Q8NI27 | THOC2 | mRNA processing | 0 | 0 | 5 | 5 | 0 | 3 |
| Monomer Ubv-specific | ||||||||
| O95479 | H6PD | Glucose dehydrogenase | 0 | 0 | 203 | 0 | 143 | 0 |
| Q9UIV8 | PI13 | Peptidase inhibitor | 0 | 0 | 146 | 0 | 120 | 0 |
| Q96QC0 | PPP1R10 | Phosphatase | 0 | 0 | 6 | 0 | 6 | 0 |
| Dimer Ubv-specific | ||||||||
| Q15233 | NONO | mRNA processing | 0 | 0 | 0 | 118 | 3 | 114 |
| Q8WXF1 | PSPC1 | mRNA processing | 3 | 0 | 0 | 56 | 0 | 51 |
| P23246 | SFPQ | mRNA processing | 5 | 2 | 0 | 60 | 2 | 70 |
| Q15691 | MAPRE1 | Microtubule binding | 0 | 0 | 0 | 58 | 0 | 48 |
| P17980 | PSMC3 | 26S proteasome subunit | 0 | 0 | 0 | 39 | 0 | 37 |
| Q9P2E9 | RRBP1 | Ribosome receptor | 0 | 0 | 0 | 13 | 0 | 28 |
| Q9Y490 | TLN1 | Cytoskeletal component | 0 | 0 | 2 | 38 | 0 | 10 |
| P42566 | EPS15 | EGFR substrate | 0 | 0 | 0 | 20 | 0 | 27 |
| Q9UII2 | ATPIF1 | ATPase inhibitor | 0 | 0 | 0 | 27 | 0 | 19 |
| O00233 | PSMD9 | 26S proteasome subunit | 0 | 0 | 0 | 14 | 0 | 21 |
| P05787 | KRT8 | Keratin | 0 | 0 | 0 | 20 | 0 | 18 |
| Q16204 | CCDC6 | Unknown | 0 | 0 | 0 | 18 | 0 | 13 |
| Q15019 | SEPT2 | Cytoskeletal GTPase | 0 | 0 | 0 | 15 | 0 | 10 |
| Q14203 | DCTN1 | Microtubule transport | 0 | 0 | 0 | 9 | 0 | 17 |
| P46736 | BRCC3 | Lys-63 deubiquitinase | 0 | 0 | 0 | 15 | 0 | 16 |
| P80303 | NUCB2 | Calcium homeostasis | 0 | 0 | 0 | 8 | 0 | 14 |
| Q07065 | CKAP4 | Cytoskeleton associated | 0 | 0 | 0 | 14 | 0 | 12 |
| P31146 | CORO1A | Cytoskeletal component | 0 | 0 | 0 | 12 | 0 | 7 |
| O60271 | SPAG9 | Scaffold protein | 0 | 0 | 0 | 9 | 0 | 13 |
| Q9BW19 | KIFC1 | Microtubule transport | 0 | 0 | 0 | 5 | 0 | 13 |
| P16220 | CREB1 | Transcription factor | 0 | 0 | 0 | 8 | 0 | 10 |
| Q13625 | TP53BP2 | p53 regulator | 0 | 0 | 0 | 5 | 0 | 8 |
| O00139 | KIF2A | Microtubule transport | 0 | 0 | 0 | 9 | 0 | 7 |
| O43293 | DAPK3 | Serine/Threonine kinase | 0 | 0 | 0 | 9 | 0 | 6 |
| Q9NVA2 | SEPT 11 | Cytoskeletal GTPase | 0 | 0 | 0 | 8 | 0 | 9 |
| Q13976 | PRKG1 | Serine/Threonine kinase | 0 | 0 | 0 | 7 | 0 | 9 |
| Q14141 | SEPT6 | Cytoskeletal GTPase | 0 | 0 | 0 | 4 | 0 | 8 |
| Q9P0K7 | RAI14 | Actin associated | 0 | 0 | 0 | 2 | 0 | 7 |
| Q16181 | SEPT7 | Cytoskeletal GTPase | 0 | 0 | 0 | 10 | 0 | 10 |
| Q14980 | NUMA1 | Nuclear matrix | 0 | 0 | 0 | 4 | 0 | 10 |
| Q96CN9 | GCC1 | Golgi associated | 0 | 0 | 0 | 4 | 0 | 7 |
| P40222 | TXLNA | Vesicle traffic | 0 | 0 | 0 | 3 | 0 | 7 |
| O95396 | MOCS3 | tRNA biosynthesis | 0 | 0 | 0 | 2 | 0 | 7 |
| Q9UPY8 | MAPRE3 | Microtubule associated | 0 | 0 | 0 | 2 | 0 | 7 |
| P62195 | PSMC5 | 26S proteasome subunit | 0 | 0 | 0 | 6 | 0 | 3 |
| Q8N302 | AGGF1 | Angiogenic factor | 0 | 0 | 0 | 2 | 0 | 6 |
| Q15390 | MTFR1 | Mitochondrial fission | 0 | 0 | 0 | 0 | 0 | 6 |
| O75146 | HIP1R | Clathrin associated | 0 | 0 | 0 | 5 | 0 | 3 |
| P53621 | COPA | Golgi-to-ER transport | 0 | 0 | 0 | 5 | 0 | 2 |
| O60308 | KIAA0562 | Centrosomal protein | 0 | 0 | 0 | 5 | 0 | 2 |
| Q969V6 | MKL1 | Transcription factor | 0 | 0 | 0 | 4 | 0 | 5 |
| Q15007 | WTAP | mRNA processing | 0 | 0 | 0 | 2 | 0 | 5 |
| Q8TBA6 | GOLGA5 | Golgi formation | 0 | 0 | 0 | 2 | 0 | 5 |
| Q4VCS5 | AMOT | Tight junction maintenance | 0 | 0 | 0 | 0 | 0 | 5 |
| Q9H6D7 | HAUS4 | Spindle assembly | 0 | 0 | 0 | 0 | 0 | 5 |
| Ubv.Fw11.2 specific | ||||||||
| Q9U.K.B1 | FBXW11 | F-box | 0 | 0 | 0 | 0 | 125 | 85 |
| Q9Y297 | FBXW1 | F-box | 0 | 0 | 0 | 0 | 10 | 4 |
| P0C0L4 | C4A | Complement comp. | 0 | 0 | 0 | 0 | 13 | 3 |
| Q06203 | PPAT | Ribosyl transferase | 0 | 0 | 0 | 0 | 13 | 3 |
| P04632 | CAPNS1 | Protease subunit | 0 | 0 | 0 | 0 | 12 | 0 |
| Q96K76 | USP47¶ | Ubiquitin protease | 0 | 0 | 0 | 0 | 3 | 7 |
| Q01664 | TFAP4 | Transcription factor | 0 | 0 | 0 | 0 | 6 | 0 |
| Ubv.Fw7.5 specific | ||||||||
| Q9U.K.T8 | FBXW2 | F-box | 0 | 0 | 24 | 18 | 0 | 0 |
| P19838 | NFKB1 | Transcription factor | 0 | 0 | 22 | 0 | 0 | 0 |
| Q13309 | SKP2 | F-box | 0 | 0 | 12 | 7 | 0 | 0 |
| Q7Z6M2 | FBXO33 | F-box | 0 | 0 | 3 | 7 | 0 | 0 |
| Q9NVF7 | FBXO28 | F-box | 0 | 0 | 0 | 7 | 0 | 0 |
| Q969H0 | FBXW7 | F-box | 0 | 0 | 5 | 0 | 0 | 0 |
| O94952 | FBXO21 | F-box | 0 | 0 | 3 | 5 | 0 | 0 |
*
ID for identified proteins showing >twofold enrichment relative to control and five peptides or more in any of the Ubv samples.
†
Gene name for identified proteins showing >twofold enrichment relative to control and five peptides or more in any of the Ubv samples.
‡
Controls correspond to HEK293T cells transfected with empty vector (V) or Ub Δ75G76G (Ub).
§
Numbers of endogenous peptides corresponding to the identified protein.
¶
USP47 is a known interactor of Fbw1 and Fbw11 (30).