8DAT: Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex
Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (intB). Determined by electron microscopy at 3.8 Å resolution. Released 30 Nov 2022.
- Method
- Electron microscopy
- Resolution
- 3.8 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 11
- Atoms
- 34,635
- Mol. weight
- 691.84 kDa
- Ligands
- ZN, ADP, ATP
- Released
- 30 Nov 2022
Explore 8DAT in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8DAT contains 262 α-helices and 173 β-strands across 11 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 45 helices, 32 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 35-40 | 6 | 1 |
| β-strand | 48-51 | 4 | 1 |
| α-helix | 53-59 | 7 | |
| β-strand | 66-70 | 5 | 1 |
| β-strand | 76-83 | 8 | 1 |
| α-helix | 88 | 1 | |
| β-strand | 91-94 | 4 | 1 |
| α-helix | 96-102 | 7 | |
| β-strand | 109-114 | 6 | 1 |
| β-strand | 119-120 | 2 | 2 |
| β-strand | 123-128 | 6 | 3 |
| β-strand | 129 | 1 | 4 |
| α-helix | 130-133 | 4 | |
| α-helix | 140 | 1 | |
| α-helix | 141-145 | 5 | |
| α-helix | 146-148 | 3 | |
| β-strand | 155-156 | 2 | 2 |
| β-strand | 161-166 | 6 | 3 |
| β-strand | 169-179 | 11 | 3 |
| β-strand | 184-185 | 2 | 2 |
| β-strand | 191-193 | 3 | 3 |
| β-strand | 199 | 1 | 4 |
| α-helix | 203-206 | 4 | |
| α-helix | 213-215 | 3 | |
| α-helix | 221-235 | 15 | |
| α-helix | 238-243 | 6 | |
| β-strand | 251-254 | 4 | 5 |
| α-helix | 261-272 | 12 | |
| β-strand | 275-278 | 4 | 5 |
| α-helix | 281-284 | 4 | |
| α-helix | 292-304 | 13 | |
| β-strand | 309-313 | 5 | 5 |
| α-helix | 316-319 | 4 | |
| α-helix | 329-343 | 15 | |
| β-strand | 351-357 | 7 | 5 |
| α-helix | 360-362 | 3 | |
| α-helix | 365-367 | 3 | |
| β-strand | 369 | 1 | 6 |
| β-strand | 372 | 1 | 6 |
| β-strand | 375-378 | 4 | 5 |
| α-helix | 384-394 | 11 | |
| β-strand | 400 | 1 | 7 |
| α-helix | 406-412 | 7 | |
| α-helix | 418-436 | 19 | |
| α-helix | 437-439 | 3 | |
| α-helix | 449-453 | 5 | |
| β-strand | 457 | 1 | 7 |
| α-helix | 459-467 | 9 | |
| α-helix | 473-475 | 3 | |
| β-strand | 480 | 1 | 8 |
| α-helix | 493-499 | 7 | |
| α-helix | 500-504 | 5 | |
| α-helix | 505-508 | 4 | |
| α-helix | 510-516 | 7 | |
| α-helix | 519-521 | 3 | |
| β-strand | 524-527 | 4 | 8 |
| α-helix | 535-545 | 11 | |
| β-strand | 548-552 | 5 | 8 |
| α-helix | 554-562 | 9 | |
| α-helix | 569-578 | 10 | |
| β-strand | 582-586 | 5 | 8 |
| α-helix | 589-591 | 3 | |
| α-helix | 609-619 | 11 | |
| β-strand | 627-633 | 7 | 8 |
| α-helix | 641-644 | 4 | |
| β-strand | 651-654 | 4 | 8 |
| α-helix | 656-658 | 3 | |
| α-helix | 660-670 | 11 | |
| α-helix | 671-673 | 3 | |
| α-helix | 675 | 1 | |
| β-strand | 676 | 1 | 9 |
| α-helix | 677 | 1 | |
| α-helix | 683-688 | 6 | |
| α-helix | 694-718 | 25 | |
| β-strand | 753 | 1 | 9 |
| α-helix | 755-763 | 9 | |
| α-helix | 771-785 | 15 | |
Chain B: 35 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 97-102 | 6 | |
| α-helix | 213-215 | 3 | |
| α-helix | 220-235 | 16 | |
| α-helix | 238-243 | 6 | |
| β-strand | 251-254 | 4 | 10 |
| α-helix | 261-272 | 12 | |
| β-strand | 275-280 | 6 | 10 |
| α-helix | 281-285 | 5 | |
| α-helix | 288 | 1 | |
| α-helix | 294-305 | 12 | |
| β-strand | 309-314 | 6 | 10 |
| α-helix | 316-319 | 4 | |
| α-helix | 329-345 | 17 | |
| β-strand | 351-356 | 6 | 10 |
| α-helix | 365-367 | 3 | |
| β-strand | 375-378 | 4 | 10 |
| α-helix | 384-394 | 11 | |
| β-strand | 400 | 1 | 11 |
| α-helix | 406-412 | 7 | |
| α-helix | 418-436 | 19 | |
| α-helix | 437-439 | 3 | |
| α-helix | 449-453 | 5 | |
| β-strand | 457 | 1 | 11 |
| α-helix | 459-468 | 10 | |
| α-helix | 473-475 | 3 | |
| β-strand | 480 | 1 | 12 |
| α-helix | 493-499 | 7 | |
| α-helix | 500-504 | 5 | |
| α-helix | 505-508 | 4 | |
| α-helix | 510-516 | 7 | |
| α-helix | 518-521 | 4 | |
| β-strand | 523-527 | 5 | 12 |
| α-helix | 534-544 | 11 | |
| β-strand | 548-552 | 5 | 12 |
| α-helix | 554-561 | 8 | |
| α-helix | 569-578 | 10 | |
| β-strand | 582-587 | 6 | 12 |
| α-helix | 589-591 | 3 | |
| α-helix | 609-619 | 11 | |
| β-strand | 627-633 | 7 | 12 |
| α-helix | 641-644 | 4 | |
| β-strand | 651-654 | 4 | 12 |
| α-helix | 656-659 | 4 | |
| α-helix | 660-670 | 11 | |
| α-helix | 683-688 | 6 | |
| α-helix | 694-718 | 25 | |
| α-helix | 755-762 | 8 | |
| α-helix | 771-786 | 16 | |
Chain C: 47 helices, 33 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 35-37 | 3 | 13 |
| α-helix | 38 | 1 | |
| β-strand | 40 | 1 | 14 |
| β-strand | 48-51 | 4 | 13 |
| α-helix | 53-59 | 7 | |
| β-strand | 66-70 | 5 | 13 |
| β-strand | 76-83 | 8 | 13 |
| α-helix | 88 | 1 | |
| β-strand | 91-93 | 3 | 13 |
| β-strand | 94 | 1 | 14 |
| α-helix | 96-102 | 7 | |
| β-strand | 109-114 | 6 | 13 |
| α-helix | 118-119 | 2 | |
| β-strand | 120 | 1 | 15 |
| β-strand | 123-128 | 6 | 16 |
| β-strand | 129 | 1 | 17 |
| α-helix | 130-133 | 4 | |
| α-helix | 140 | 1 | |
| α-helix | 141-145 | 5 | |
| α-helix | 146-149 | 4 | |
| β-strand | 155-157 | 3 | 15 |
| β-strand | 161-166 | 6 | 16 |
| β-strand | 169-179 | 11 | 16 |
| β-strand | 183-185 | 3 | 15 |
| β-strand | 191-193 | 3 | 16 |
| α-helix | 197-198 | 2 | |
| β-strand | 199 | 1 | 17 |
| α-helix | 200 | 1 | |
| α-helix | 202-206 | 5 | |
| α-helix | 213-215 | 3 | |
| α-helix | 220-235 | 16 | |
| α-helix | 238-243 | 6 | |
| β-strand | 250-254 | 5 | 18 |
| α-helix | 261-272 | 12 | |
| β-strand | 275-276 | 2 | 18 |
| β-strand | 279 | 1 | 18 |
| α-helix | 281-285 | 5 | |
| α-helix | 288 | 1 | |
| α-helix | 292-305 | 14 | |
| β-strand | 309-313 | 5 | 18 |
| α-helix | 316-318 | 3 | |
| α-helix | 329-344 | 16 | |
| β-strand | 351-357 | 7 | 18 |
| α-helix | 365-367 | 3 | |
| β-strand | 376-378 | 3 | 18 |
| α-helix | 384-394 | 11 | |
| β-strand | 400 | 1 | 19 |
| α-helix | 406-412 | 7 | |
| α-helix | 418-436 | 19 | |
| α-helix | 437-439 | 3 | |
| α-helix | 449-454 | 6 | |
| β-strand | 457 | 1 | 19 |
| α-helix | 459-467 | 9 | |
| α-helix | 473-475 | 3 | |
| β-strand | 480 | 1 | 20 |
| α-helix | 493-499 | 7 | |
| α-helix | 500-504 | 5 | |
| α-helix | 505-508 | 4 | |
| α-helix | 510-516 | 7 | |
| α-helix | 519-521 | 3 | |
| β-strand | 524-527 | 4 | 20 |
| α-helix | 534-544 | 11 | |
| β-strand | 548-552 | 5 | 20 |
| α-helix | 554-562 | 9 | |
| α-helix | 569-578 | 10 | |
| β-strand | 582-586 | 5 | 20 |
| α-helix | 589-591 | 3 | |
| α-helix | 609-620 | 12 | |
| β-strand | 627-633 | 7 | 20 |
| α-helix | 636-638 | 3 | |
| α-helix | 641-644 | 4 | |
| β-strand | 651-654 | 4 | 20 |
| α-helix | 656-658 | 3 | |
| α-helix | 660-670 | 11 | |
| β-strand | 676 | 1 | 21 |
| α-helix | 683-688 | 6 | |
| α-helix | 694-718 | 25 | |
| β-strand | 753 | 1 | 21 |
| α-helix | 755-763 | 9 | |
| α-helix | 771-787 | 17 | |
Chain D: 34 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 97-102 | 6 | |
| α-helix | 201-205 | 5 | |
| α-helix | 213-215 | 3 | |
| α-helix | 220-235 | 16 | |
| α-helix | 237-243 | 7 | |
| β-strand | 250-254 | 5 | 22 |
| α-helix | 261-272 | 12 | |
| β-strand | 275-280 | 6 | 22 |
| α-helix | 281-285 | 5 | |
| α-helix | 292-305 | 14 | |
| β-strand | 309-314 | 6 | 22 |
| α-helix | 316-318 | 3 | |
| α-helix | 329-345 | 17 | |
| β-strand | 351-357 | 7 | 22 |
| α-helix | 365-367 | 3 | |
| β-strand | 375-378 | 4 | 22 |
| α-helix | 384-394 | 11 | |
| β-strand | 400 | 1 | 23 |
| α-helix | 406-412 | 7 | |
| α-helix | 418-436 | 19 | |
| α-helix | 437-439 | 3 | |
| α-helix | 449-452 | 4 | |
| β-strand | 457 | 1 | 23 |
| α-helix | 459-468 | 10 | |
| α-helix | 473-475 | 3 | |
| β-strand | 479-480 | 2 | 24 |
| α-helix | 493-499 | 7 | |
| α-helix | 500-504 | 5 | |
| α-helix | 505-508 | 4 | |
| α-helix | 510-516 | 7 | |
| α-helix | 519-521 | 3 | |
| β-strand | 523-527 | 5 | 24 |
| α-helix | 534-544 | 11 | |
| β-strand | 548-552 | 5 | 24 |
| α-helix | 554-562 | 9 | |
| α-helix | 569-578 | 10 | |
| β-strand | 582-586 | 5 | 24 |
| α-helix | 609-619 | 11 | |
| β-strand | 627-633 | 7 | 24 |
| α-helix | 641-644 | 4 | |
| β-strand | 651-654 | 4 | 24 |
| α-helix | 656-658 | 3 | |
| α-helix | 660-670 | 11 | |
| α-helix | 683-688 | 6 | |
| α-helix | 694-718 | 25 | |
| α-helix | 755-763 | 9 | |
| α-helix | 771-786 | 16 | |
Chain E: 36 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 213-215 | 3 | |
| α-helix | 220-235 | 16 | |
| α-helix | 237-243 | 7 | |
| α-helix | 246-248 | 3 | |
| β-strand | 250-254 | 5 | 25 |
| α-helix | 261-272 | 12 | |
| β-strand | 278 | 1 | 25 |
| α-helix | 281-286 | 6 | |
| α-helix | 288 | 1 | |
| α-helix | 292-304 | 13 | |
| β-strand | 309 | 1 | 26 |
| β-strand | 312-314 | 3 | 25 |
| α-helix | 316-319 | 4 | |
| β-strand | 321 | 1 | 27 |
| α-helix | 331-343 | 13 | |
| β-strand | 351 | 1 | 26 |
| β-strand | 353-357 | 5 | 25 |
| β-strand | 363 | 1 | 27 |
| α-helix | 365-367 | 3 | |
| β-strand | 375-378 | 4 | 25 |
| α-helix | 384-394 | 11 | |
| β-strand | 400 | 1 | 28 |
| α-helix | 406-412 | 7 | |
| α-helix | 418-436 | 19 | |
| α-helix | 437-439 | 3 | |
| α-helix | 449-453 | 5 | |
| β-strand | 457 | 1 | 28 |
| α-helix | 459-468 | 10 | |
| α-helix | 473-475 | 3 | |
| β-strand | 479-480 | 2 | 29 |
| α-helix | 493-499 | 7 | |
| α-helix | 500-504 | 5 | |
| α-helix | 505-508 | 4 | |
| α-helix | 510-516 | 7 | |
| α-helix | 518-521 | 4 | |
| β-strand | 523-527 | 5 | 29 |
| α-helix | 534-544 | 11 | |
| β-strand | 548-552 | 5 | 29 |
| α-helix | 554-561 | 8 | |
| α-helix | 569-578 | 10 | |
| β-strand | 582-586 | 5 | 29 |
| α-helix | 589-591 | 3 | |
| α-helix | 609-619 | 11 | |
| β-strand | 627-633 | 7 | 29 |
| α-helix | 636-638 | 3 | |
| α-helix | 641-644 | 4 | |
| β-strand | 652-654 | 3 | 29 |
| α-helix | 656-658 | 3 | |
| α-helix | 660-670 | 11 | |
| β-strand | 676 | 1 | 30 |
| α-helix | 683-688 | 6 | |
| α-helix | 694-718 | 25 | |
| β-strand | 753 | 1 | 30 |
| α-helix | 755-763 | 9 | |
| α-helix | 771-786 | 16 | |
Chain F: 35 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 213-215 | 3 | |
| α-helix | 220-235 | 16 | |
| α-helix | 237-243 | 7 | |
| β-strand | 250-254 | 5 | 31 |
| α-helix | 261-272 | 12 | |
| β-strand | 275-280 | 6 | 31 |
| α-helix | 281-285 | 5 | |
| α-helix | 288 | 1 | |
| α-helix | 292-305 | 14 | |
| β-strand | 309-314 | 6 | 31 |
| α-helix | 316-318 | 3 | |
| α-helix | 323-325 | 3 | |
| α-helix | 329-344 | 16 | |
| β-strand | 351-357 | 7 | 31 |
| α-helix | 365-367 | 3 | |
| β-strand | 375-378 | 4 | 31 |
| α-helix | 380-382 | 3 | |
| α-helix | 384-394 | 11 | |
| β-strand | 400 | 1 | 32 |
| α-helix | 406-412 | 7 | |
| α-helix | 418-436 | 19 | |
| α-helix | 437-439 | 3 | |
| α-helix | 449-454 | 6 | |
| β-strand | 457 | 1 | 32 |
| α-helix | 459-467 | 9 | |
| α-helix | 473-475 | 3 | |
| β-strand | 480 | 1 | 33 |
| α-helix | 493-499 | 7 | |
| α-helix | 500-504 | 5 | |
| α-helix | 505-508 | 4 | |
| α-helix | 510-516 | 7 | |
| β-strand | 524-527 | 4 | 33 |
| α-helix | 534-544 | 11 | |
| β-strand | 548-552 | 5 | 33 |
| α-helix | 554-562 | 9 | |
| α-helix | 569-578 | 10 | |
| β-strand | 582-586 | 5 | 33 |
| α-helix | 589-591 | 3 | |
| α-helix | 609-619 | 11 | |
| β-strand | 627-633 | 7 | 33 |
| α-helix | 641-644 | 4 | |
| β-strand | 651-654 | 4 | 33 |
| α-helix | 656-659 | 4 | |
| α-helix | 660-670 | 11 | |
| β-strand | 676 | 1 | 34 |
| α-helix | 683-687 | 5 | |
| α-helix | 694-718 | 25 | |
| β-strand | 753 | 1 | 34 |
| α-helix | 755-762 | 8 | |
| α-helix | 771-787 | 17 | |
Chain G: 21 helices, 25 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 117-124 | 8 | |
| β-strand | 129 | 1 | 35 |
| α-helix | 150 | 1 | |
| β-strand | 151 | 1 | 35 |
| α-helix | 152 | 1 | |
| α-helix | 156-161 | 6 | |
| α-helix | 170-179 | 10 | |
| α-helix | 208-210 | 3 | |
| α-helix | 211-213 | 3 | |
| β-strand | 215-216 | 2 | 10 |
| α-helix | 222-223 | 2 | |
| β-strand | 224-226 | 3 | 36 |
| β-strand | 236-239 | 4 | 37 |
| α-helix | 242-255 | 14 | |
| β-strand | 260-270 | 11 | 37 |
| β-strand | 276-285 | 10 | 37 |
| β-strand | 290-291 | 2 | 38 |
| β-strand | 295-297 | 3 | 38 |
| α-helix | 300-317 | 18 | |
| β-strand | 321-327 | 7 | 37 |
| β-strand | 331 | 1 | 39 |
| β-strand | 339 | 1 | 39 |
| α-helix | 352-363 | 12 | |
| α-helix | 366-367 | 2 | |
| β-strand | 368 | 1 | 40 |
| β-strand | 376 | 1 | 40 |
| β-strand | 382-386 | 5 | 37 |
| β-strand | 396-401 | 6 | 37 |
| α-helix | 403-410 | 8 | |
| β-strand | 415-416 | 2 | 41 |
| β-strand | 417 | 1 | 42 |
| β-strand | 422-424 | 3 | 41 |
| β-strand | 429 | 1 | 43 |
| β-strand | 432 | 1 | 43 |
| β-strand | 437-442 | 6 | 36 |
| β-strand | 448-452 | 5 | 36 |
| β-strand | 456-458 | 3 | 41 |
| α-helix | 460-462 | 3 | |
| β-strand | 463-469 | 7 | 37 |
| α-helix | 501-507 | 7 | |
| α-helix | 510-514 | 5 | |
| α-helix | 517-524 | 8 | |
| α-helix | 527-536 | 10 | |
| α-helix | 541-551 | 11 | |
| α-helix | 557-565 | 9 | |
| α-helix | 567-578 | 12 | |
Chain H: 2 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 244-252 | 9 | |
| β-strand | 291 | 1 | 42 |
| β-strand | 298-300 | 3 | 38 |
| α-helix | 304-305 | 2 | |
3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cell division control protein 48 | A, B, C, D, E, F | protein | 838 | Saccharomyces cerevisiae | P25694 (AlphaFold model) |
| Nuclear protein localization protein 4 | G | protein | 583 | Saccharomyces cerevisiae | P33755 (AlphaFold model) |
| Ubiquitin fusion degradation protein 1 | H | protein | 363 | Saccharomyces cerevisiae | P53044 (AlphaFold model) |
| Ubiquitin | J, K, L | protein | 76 | Saccharomyces cerevisiae | P0CG63 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F), FASTA
>8DAT_1 Cell division control protein 48 (chains A, B, C, D, E, F)
GSHMGEEHKPLLDASGVDPREEDKTATAILRRKKKDNMLLVDDAINDDNSVIAINSNTMD
KLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPD
IKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVD
VEPEEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHP
QLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLR
KAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAAT
NRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYV
GADIASLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRET
VVESVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLL
AKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIAKARG
GSLGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPL
PDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHR
QHEAEKEVKVEGEDVEMTDEGAKAEQEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRY
EAYSQQMKASRGQFSNFNFNDAPLGTTATDNANSNNSAPSGAGAAFGSNAEEDDDLYS
Sequence of entity 2 (G), FASTA
>8DAT_2 Nuclear protein localization protein 4 (chains G)
GSHMLIRFRSKNGTHRVSCQENDLFGTVIEKLVGNLDPNADVDTFTVCEKPGQGIHAVSE
LADRTVMDLGLKHGDMLILNYSDKPANEKDGVNVEIGSVGIDSKGIRQHRYGPLRIKELA
VDEELEKEDGLIPRQKSKLCKHGDRGMCEYCSPLPPWDKEYHEKNKIKHISFHSYLKKLN
ENANKKENGSSYISPLSEPDFRINKRCHNGHEPWPRGICSKCQPSAITLQQQEFRMVDHV
EFQKSEIINEFIQAWRYTGMQRFGYMYGSYSKYDNTPLGIKAVVEAIYEPPQHDEQDGLT
MDVEQVKNEMLQIDRQAQEMGLSRIGLIFTDLSDAGAGDGSVFCKRHKDSFFLSSLEVIM
AARHQTRHPNVSKYSEQGFFSSKFVTCVISGNLEGEIDISSYQVSTEAEALVTADMISGS
TFPSMAYINDTTDERYVPEIFYMKSNEYGITVKENAKPAFPVDYLLVTLTHGFPNTDTET
NSKFVSSTGFPWSNRQAMGQSQDYQELKKYLFNVASSGDFNLLHEKISNFHLLLYINSLQ
ILSPDEWKLLIESAVKNEWEESLLKLVSSAGWQTLVMILQESG
Sequence of entity 3 (H), FASTA
>8DAT_3 Ubiquitin fusion degradation protein 1 (chains H)
GSMFSGFSSFGGGNGFVNMPQTFEEFFRCYPIAMMNDRIRKDDANFGGKIFLPPSALSKL
SMLNIRYPMLFKLTANETGRVTHGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTD
VPLGQFVKLEPQSVDFLDISDPKAVLENVLRNFSTLTVDDVIEISYNGKTFKIKILEVKP
ESSSKSICVIETDLVTDFAPPVGYVEPDYKALKAQQDKEKKNSFGKGQVLDPSVLGQGSM
STRIDYAGIANSSRNKLSKFVGQGQNISGKAPKAEPKQDIKDMKITFDGEPAKLDLPEGQ
LFFGFPMVLPKEDEESAAGSKSSEQNFQGQGISLRKSNKRKTKSDHDSSKSKAPKSPEVI
EID
Sequence of entity 4 (J, K, L), FASTA
>8DAT_4 Ubiquitin (chains J, K, L)
MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 7 |
| ATP | Adenosine-5'-triphosphate | C10 H16 N5 O13 P3 | 5 |
Primary citation
SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex. Lee, H.G., Lemmon, A.A., Lima, C.D. Proc Natl Acad Sci U S A (2023) 120:e2213703120-e2213703120. DOI 10.1073/pnas.2213703120 · PubMed
Other PDB entries of the same protein (UniProt P25694 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8UB4 2.9 Å, Cdc48-Shp1 unfolding native substrate, consensus structure
- 8DAR 3.0 Å, Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex unbound but in the presence of…
- 9OFV 3.16 Å, Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex
- 8U9P 3.2 Å, Cdc48-Shp1 unfolding native substrate, Class 2
- 8U7T 3.3 Å, Substrate-bound Cdc48, Class 1
- 8UA1 3.4 Å, Cdc48-Shp1 unfolding native substrate, Class 9
- 8UAA 3.4 Å, Cdc48-Shp1 unfolding native substrate, Class 3
- 8DAS 3.5 Å, Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubiquitin moieties in…
- 8DAV 3.5 Å, Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubiquitin moieties and one…
- 8U8I 3.5 Å, Cdc48-Shp1 unfolding native substrate, Class 4
- 8UA0 3.5 Å, Cdc48-Shp1 unfolding native substrate, Class 8
- 6OAB 3.6 Å, Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx,…
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