Table 1.
Summary of the proteins detected by BioID-Nups, BioID-LaA. and BirA*-only
| Identified candidates | BirA* fusion protein baits |
|||||||
| Nup160 | Nup133 | Nup107 | Nup85 | Nup43 | Nup53 | LaA | BirA* | |
| Nup107 complex (Y-complex + Elys) | ||||||||
| NUP160 | Bait | 0.1 | 0.1 | |||||
| NUP107 | 4.3 | Bait | 1.1 | 4.3 | ||||
| NUP133 | Bait | 7.0 | 0.4 | 0.2 | ||||
| NUP96 | 6.4 | 8.9 | 4.5 | 14.8 | 17.8 | 6.0 | 0.3 | |
| NUP85 | Bait | X | ||||||
| NUP43 | 0.4 | Bait | ||||||
| SEH1L | 0.6 | 7.7 | X | |||||
| ELYS | 14.5 | 6.9 | 1.6 | X | 0.2 | 2.2 | ||
| Percent of total that are Nup107 complex/Elys components | 21 | 20 | 14 | 24 | 23 | 6 | 3 | 0 |
| Nup93 complex | ||||||||
| NUP53 | Bait | |||||||
| NUP93 | 0.1 | |||||||
| NUP155 | 2.7 | 0.1 | ||||||
| NUP205 | 0.3 | |||||||
| NUP188 | X | 5.2 | ||||||
| Nup62 complex | ||||||||
| NUP62* | 5.6 | 17.2 | ||||||
| NUP58/45 | 7.2 | |||||||
| NUP54 | 1.6 | |||||||
| Transmembrane nups | ||||||||
| POM121 | 1.8 | 1.4 | 0.5 | 0.2 | 2.6 | 1.4 | ||
| NDC1 | 1.1 | |||||||
| Percent of total that are expected Nup53 partners | 2 | 1 | 0 | 6 | 0 | 38 | 2 | 0 |
| Cytoplasmic nups | ||||||||
| NUP88 | X | 1.9 | 1.5 | |||||
| NUP214 | 0.9 | 8.7 | 12.5 | <0.1 | ||||
| GLE1 | 0.4 | |||||||
| CG1 | 5.3 | |||||||
| DDX19B/DBP5 | 0.8 | |||||||
| Cytoplasmic filament nups | ||||||||
| RANBP2/Nup358 | 5.1 | 6.5 | 25.1 | 13.5 | 4.0 | 4.7 | 0.8 | |
| RANGAP1 | 2.6 | 2.2 | 0.1 | |||||
| Nuclear pore basket | ||||||||
| NUP153 | 17.7 | 23.1 | 23.3 | 20 | 15.2 | 8.9 | 5.1 | 0.1 |
| NUP50 | 1.2 | 2.8 | 11.7 | 16.5 | 5.4 | 1.3 | 4.4 | |
| TPR | 11.7 | 1.2 | ||||||
| SENP1 | 1.2 | 1.0 | 1.3 | |||||
| SENP2 | 6.7 | 1.3 | 5.2 | |||||
| NUP98 | 0.4 | 0.5 | 6.0 | 0.4 | ||||
| Import/export | ||||||||
| KPNB1 | 0.3 | 0.1 | ||||||
| XPO1 | 0.3 | |||||||
| Percent of total that are NPC-associated | 47 | 61 | 92 | 94 | 54 | 86 | 15 | 2 |
| Nuclear envelope constituents | ||||||||
| TMPO beta | 25.9 | 28.9 | 4.3 | 12.7 | 1.3 | |||
| LEMD3 | 3.5 | 0.6 | 3.7 | <0.1 | ||||
| EMD | 1.5 | 8.9 | ||||||
| SYNE1 | 0.0 | 0.0 | ||||||
| TMEM201 | 0.3 | 0.3 | ||||||
| TMPO alpha | 0.6 | |||||||
| LBR | 0.2 | |||||||
| Percent of total that are NPC/NE-associated | 76 | 90 | 92 | 94 | 54 | 92 | 41 | 4 |
Numbers are the percent of total adjusted peptides (excluding BirA*-fusion protein). Candidates listed as 0.0 are <0.1. Numbers in bold indicate proteins identified by XL-MS on isolated Y complex or intact NPC. X, proteins identified by XL-MS but not BioID. BioID pull-down for LaA was performed with asynchronous cells.