Table 2.
Mass spectrometric identification of proteins that co-purify with cytosolic and synaptic 26S proteasomes.
| IPI identifier | Unigene identifier | Gene name | Gene symbol | Cytosolic 26S | Synaptic 26S | ||
|---|---|---|---|---|---|---|---|
| Unique peptidesa | Sequence coverage (%) | Unique peptidesa | Sequence coverage (%) | ||||
| SUBSTOICHIOMETRIC PROTEASOME PROTEIN | |||||||
| IPI00367234.3 | Rn.154631 | Proteasome-associated protein ECM29 | Ecm29 | 6 | 5 | 0 | 0 |
| IPI00204510.5 | Rn.9320 | 26S proteasome subunit Rpn13/ADRM1 | Adrm1 | 3 | 6 | 3 | 6 |
| IPI00200601.2 | Rn.40430 | Thioredoxin-like protein 1/TRP32 | Txnl1 | 13 | 56 | 14 | 60 |
| 19S ASSEMBLY FACTOR | |||||||
| IPI00194471.1 | Rn.13415 | 26S proteasome non-ATPase subunit 5/S5b | Psmd5 | 14 | 38 | 13 | 37 |
| IPI00231038.4 | Rn.24127 | 26S proteasome non-ATPase subunit 9/Bridge-1/p27 | Psmd9 | 5 | 24 | 5 | 24 |
| E3 | |||||||
| IPI00201213.3 | Rn.12130 | HECT, UBA and WWE domain-containing 1/ARF-BP1 | Huwe1 | 51 | 21 | 54 | 21 |
| IPI00365749.3 | Rn.198497 | Isoform 2 of ubiquitin-protein ligase E3A/E6-AP | Ube3a | 20 | 27 | 16 | 24 |
| IPI00768915.1 | n/a | Potassium channel modulatory factor 1 | Kcmf1 | 4 | 27 | 4 | 23 |
| DUB | |||||||
| IPI00734588.1 | Rn.40424 | Ubiquitin carboxyl-terminal hydrolase L5/UCH37 | Uchl5 | 7 | 26 | 5 | 23 |
| IPI00207657.1 | Rn.44078 | Ubiquitin specific protease 5/isopeptidase T | Usp5 | 33 | 46 | 38 | 48 |
| IPI00372303.3 | Rn.72721 | Ubiquitin specific protease 7/HAUSP | Usp7 | 8 | 13 | 12 | 17 |
| IPI00367362.3 | n/a | Ubiquitin specific protease 13 | Usp13 | 9 | 26 | 8 | 24 |
| IPI00204532.2 | Rn.11790 | Ubiquitin specific protease 14 | Usp14 | 20 | 43 | 17 | 37 |
| UPS | |||||||
| IPI00382052.2 | Rn.3474 | Isoform 2 of TAX1-binding protein 1/T6BP | Tax1bp1 | 0 | 0 | 3 | 6 |
| IPI00194561.1 | Rn.107103 | Isoform 1 of sequestosome-1/p62 | Sqstm1 | 6 | 28 | 5 | 17 |
| N-END RULE | |||||||
| IPI00359416.3 | Rn.37755 | Retinoblastoma protein associated factor p600/RBAF600/UBR4 | Ubr4 | 66 | 18 | 74 | 19 |
| VCP COMPLEX | |||||||
| IPI00212014.2 | Rn.98891 | Valosin-containing protein/p97 | Vcp | 18 | 28 | 30 | 41 |
| IPI00204786.1 | Rn.203087 | Fas-associated factor 1 | Faf1 | 11 | 23 | 11 | 21 |
| CHAPERONE | |||||||
| IPI00207355.3 | Rn.211303 | Heat shock-related 70 kDa protein 2 | Hspa2 | 4 | 9 | 4 | 9 |
| VESICLE | |||||||
| IPI00204644.1 | Rn.107689 | Isoform B of synaptosomal-associated protein 25 | Snap25 | 0 | 0 | 11 | 50 |
| IPI00394488.2 | Rn.203179 | Glioblastoma amplified sequence/NIPSNAP2 | Gbas | 6 | 31 | 6 | 26 |
| CYTOSKELETON | |||||||
| IPI00231407.4 | Rn.11247 | Isoform A of drebrin | Dbn1 | 0 | 0 | 1 | 4 |
| IPI00197579.1 | Rn.2458 | Isoform 1 of tubulin beta 5 | Tubb5 | 5 | 17 | 4 | 15 |
| IPI00195673.1 | Rn.98430 | Tubulin beta 6 | Tubb6 | 4 | 13 | 3 | 10 |
| PHOSPHOPROTEIN BINDING | |||||||
| IPI00230835.4 | Rn.29936 | 14-3-3 protein gamma | Ywhag | 0 | 0 | 1 | 6 |
| IPI00324893.4 | Rn.1292 | 14-3-3 protein zeta/delta | Ywhaz | 1 | 6 | 1 | 6 |
| RASGEF | |||||||
| IPI00200118.4 | Rn.53868 | Isoform 2 of GRIP1-associated protein 1/GRASP-1 | Gripap1 | 0 | 0 | 1 | 2 |
| UNKNOWN | |||||||
| IPI00188755.4 | Rn.106046 | Caspase recruitment domain-containing protein | Fam188a | 4 | 12 | 4 | 14 |
| CLATHRIN COMPLEXb | |||||||
| IPI00193983.1 | Rn.3589 | Clathrin heavy chain | Cltc | 0 | 0 | 12 | 11 |
| IPI00203346.4 | n/a | AP-2 complex subunit alpha-1 | Ap2a1 | 0 | 0 | 1 | 2 |
| IPI00471901.3 | Rn.34928 | AP-2 complex subunit alpha-2 | Ap2a2 | 0 | 0 | 3 | 6 |
| IPI00231502.3 | Rn.56138 | Isoform 2 of AP-2 complex subunit beta-1 | Ap2b1 | 0 | 0 | 2 | 2 |
| IPI00196530.1 | Rn.3172 | AP-2 complex subunit mu-1 | Ap2m1 | 0 | 0 | 2 | 6 |
| IPI00358691.2 | Rn.162085 | Epidermal growth factor receptor pathway substrate 15 isoform B | Eps15 | 0 | 0 | 3 | 6 |
| MITOCHONDRIAc | |||||||
| IPI00196750.1 | Rn.106922 | Single-stranded DNA-binding protein, mitochondrial | Ssbp1 | 0 | 0 | 4 | 40 |
auniqueness is defined solely by peptide sequence.
bThe clathrin complex appears to directly bind to GST-UBL independent of proteasome.
cMitochondrial proteins may be contaminants of synaptosomes.