6OAB: Cell division control protein 48
Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 2. Determined by electron microscopy at 3.6 Å resolution. Released 3 Jul 2019.
- Method
- Electron microscopy
- Resolution
- 3.6 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 6
- Atoms
- 19,690
- Mol. weight
- 467.06 kDa
- Ligands
- BEF, ADP
- Released
- 3 Jul 2019
Explore 6OAB in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6OAB contains 128 α-helices and 68 β-strands across 6 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: 27 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 220-223 | 4 | |
| α-helix | 231-235 | 5 | |
| β-strand | 251-254 | 4 | 17 |
| α-helix | 263-271 | 9 | |
| β-strand | 277-278 | 2 | 18 |
| α-helix | 282-284 | 3 | |
| α-helix | 294-305 | 12 | |
| β-strand | 309-312 | 4 | 18 |
| β-strand | 314 | 1 | 17 |
| α-helix | 330-334 | 5 | |
| α-helix | 337-344 | 8 | |
| β-strand | 351-353 | 3 | 18 |
| β-strand | 356 | 1 | 17 |
| α-helix | 365-367 | 3 | |
| β-strand | 375-378 | 4 | 17 |
| α-helix | 379-381 | 3 | |
| α-helix | 387-392 | 6 | |
| α-helix | 406-412 | 7 | |
| α-helix | 421-435 | 15 | |
| α-helix | 459-463 | 5 | |
| α-helix | 464-466 | 3 | |
| α-helix | 479-482 | 4 | |
| α-helix | 494-508 | 15 | |
| α-helix | 511-516 | 6 | |
| α-helix | 518-521 | 4 | |
| β-strand | 524-527 | 4 | 19 |
| α-helix | 536-543 | 8 | |
| β-strand | 548-551 | 4 | 19 |
| α-helix | 554-556 | 3 | |
| α-helix | 564-577 | 14 | |
| β-strand | 582-587 | 6 | 19 |
| α-helix | 590-593 | 4 | |
| α-helix | 610-617 | 8 | |
| β-strand | 628-632 | 5 | 19 |
| α-helix | 636-638 | 3 | |
| β-strand | 651-654 | 4 | 19 |
| α-helix | 663-670 | 8 | |
| α-helix | 683-688 | 6 | |
| β-strand | 690 | 1 | 20 |
| β-strand | 692 | 1 | 20 |
| α-helix | 696-715 | 20 | |
Chain B: 24 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 220-227 | 8 | |
| α-helix | 231-235 | 5 | |
| β-strand | 251-254 | 4 | 10 |
| α-helix | 263-267 | 5 | |
| β-strand | 275-279 | 5 | 10 |
| α-helix | 292-305 | 14 | |
| β-strand | 309-314 | 6 | 10 |
| α-helix | 334-344 | 11 | |
| β-strand | 354-356 | 3 | 10 |
| α-helix | 360-362 | 3 | |
| α-helix | 365-367 | 3 | |
| β-strand | 377-378 | 2 | 10 |
| α-helix | 380-382 | 3 | |
| α-helix | 388-394 | 7 | |
| α-helix | 406-412 | 7 | |
| α-helix | 420-435 | 16 | |
| α-helix | 459-465 | 7 | |
| α-helix | 472-474 | 3 | |
| α-helix | 496-508 | 13 | |
| α-helix | 512-516 | 5 | |
| α-helix | 518-521 | 4 | |
| β-strand | 524-527 | 4 | 11 |
| α-helix | 536-542 | 7 | |
| β-strand | 548-552 | 5 | 11 |
| α-helix | 564-578 | 15 | |
| β-strand | 582-587 | 6 | 11 |
| α-helix | 589-591 | 3 | |
| α-helix | 594-596 | 3 | |
| α-helix | 607-619 | 13 | |
| β-strand | 628-633 | 6 | 11 |
| β-strand | 651-654 | 4 | 11 |
| α-helix | 660-670 | 11 | |
| α-helix | 683-688 | 6 | |
| α-helix | 696-715 | 20 | |
Chain C: 25 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 224-230 | 7 | |
| α-helix | 232-235 | 4 | |
| α-helix | 246-248 | 3 | |
| β-strand | 252-254 | 3 | 12 |
| α-helix | 264-267 | 4 | |
| β-strand | 275-280 | 6 | 12 |
| α-helix | 291-305 | 15 | |
| β-strand | 309-314 | 6 | 12 |
| α-helix | 316-318 | 3 | |
| α-helix | 331-337 | 7 | |
| β-strand | 352-356 | 5 | 12 |
| α-helix | 365-367 | 3 | |
| β-strand | 376-378 | 3 | 12 |
| α-helix | 389-392 | 4 | |
| β-strand | 400 | 1 | 13 |
| α-helix | 406-410 | 5 | |
| α-helix | 420-434 | 15 | |
| β-strand | 457 | 1 | 13 |
| α-helix | 462-465 | 4 | |
| α-helix | 475-477 | 3 | |
| α-helix | 493-508 | 16 | |
| α-helix | 511-516 | 6 | |
| β-strand | 523-526 | 4 | 14 |
| α-helix | 540-543 | 4 | |
| β-strand | 548-553 | 6 | 14 |
| β-strand | 561 | 1 | 15 |
| α-helix | 564-578 | 15 | |
| β-strand | 582-587 | 6 | 14 |
| α-helix | 589-591 | 3 | |
| α-helix | 609-615 | 7 | |
| α-helix | 616-620 | 5 | |
| β-strand | 627-632 | 6 | 14 |
| β-strand | 651-653 | 3 | 14 |
| α-helix | 668-671 | 4 | |
| β-strand | 678 | 1 | 16 |
| β-strand | 680 | 1 | 16 |
| α-helix | 683-687 | 5 | |
| α-helix | 696-710 | 15 | |
| α-helix | 755-759 | 5 | |
| α-helix | 771-774 | 4 | |
Chain D: 26 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 223-235 | 13 | |
| α-helix | 246-248 | 3 | |
| β-strand | 250-254 | 5 | 1 |
| α-helix | 264-272 | 9 | |
| β-strand | 275-279 | 5 | 1 |
| α-helix | 294-304 | 11 | |
| β-strand | 309-314 | 6 | 1 |
| β-strand | 321 | 1 | 2 |
| α-helix | 331-340 | 10 | |
| β-strand | 351-356 | 6 | 1 |
| α-helix | 360-362 | 3 | |
| β-strand | 363 | 1 | 2 |
| β-strand | 377-378 | 2 | 1 |
| α-helix | 387-391 | 5 | |
| α-helix | 419-435 | 17 | |
| α-helix | 459-466 | 8 | |
| α-helix | 472-474 | 3 | |
| α-helix | 493-503 | 11 | |
| α-helix | 505-508 | 4 | |
| α-helix | 511-516 | 6 | |
| α-helix | 519-521 | 3 | |
| β-strand | 525-526 | 2 | 3 |
| β-strand | 527 | 1 | 4 |
| α-helix | 536-540 | 5 | |
| β-strand | 548-552 | 5 | 3 |
| β-strand | 561 | 1 | 5 |
| α-helix | 567-577 | 11 | |
| β-strand | 582-587 | 6 | 3 |
| α-helix | 589-591 | 3 | |
| α-helix | 609-615 | 7 | |
| α-helix | 616-620 | 5 | |
| α-helix | 623-624 | 2 | |
| β-strand | 627-632 | 6 | 3 |
| β-strand | 654 | 1 | 4 |
| α-helix | 665-669 | 5 | |
| α-helix | 683-688 | 6 | |
| α-helix | 694-697 | 4 | |
| α-helix | 702-707 | 6 | |
| α-helix | 710-713 | 4 | |
| α-helix | 771-774 | 4 | |
Chain E: 26 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 221-226 | 6 | |
| α-helix | 227-231 | 5 | |
| α-helix | 232-235 | 4 | |
| α-helix | 237-240 | 4 | |
| β-strand | 250-254 | 5 | 6 |
| α-helix | 262-272 | 11 | |
| β-strand | 275-276 | 2 | 7 |
| α-helix | 281-284 | 4 | |
| α-helix | 291-293 | 3 | |
| α-helix | 297-305 | 9 | |
| β-strand | 309-310 | 2 | 7 |
| β-strand | 314 | 1 | 6 |
| α-helix | 331-334 | 4 | |
| α-helix | 337-341 | 5 | |
| β-strand | 353-356 | 4 | 6 |
| β-strand | 376-378 | 3 | 6 |
| α-helix | 387-394 | 8 | |
| α-helix | 406-412 | 7 | |
| α-helix | 422-435 | 14 | |
| α-helix | 459-467 | 9 | |
| α-helix | 472-474 | 3 | |
| α-helix | 482 | 1 | |
| α-helix | 493-502 | 10 | |
| α-helix | 505-508 | 4 | |
| α-helix | 510-516 | 7 | |
| β-strand | 523-527 | 5 | 8 |
| α-helix | 537-544 | 8 | |
| β-strand | 548-551 | 4 | 8 |
| β-strand | 561 | 1 | 9 |
| α-helix | 567-578 | 12 | |
| β-strand | 582-586 | 5 | 8 |
| α-helix | 589-591 | 3 | |
| α-helix | 609-615 | 7 | |
| β-strand | 627-632 | 6 | 8 |
| α-helix | 641-644 | 4 | |
| β-strand | 649-654 | 6 | 8 |
| α-helix | 655 | 1 | |
| α-helix | 660-663 | 4 | |
Chain H: 0 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2 | 1 | 9 |
| β-strand | 4 | 1 | 5 |
| β-strand | 6 | 1 | 15 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cell division control protein 48 | A, B, C, D, E | protein | 835 | Saccharomyces cerevisiae | P25694 (AlphaFold model) |
| poly(alanine) substrate | H | protein | 24 | Saccharomyces cerevisiae | |
Sequence of entity 1 (A, B, C, D, E), FASTA
>6OAB_1 Cell division control protein 48 (chains A, B, C, D, E)
MGEEHKPLLDASGVDPREEDKTATAILRRKKKDNMLLVDDAINDDNSVIAINSNTMDKLE
LFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKY
ATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEP
EEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLF
KAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAF
EEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRP
NSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGAD
IASLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVE
SVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKA
VATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSL
GDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDE
NARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHE
AEKEVKVEGEDVEMTDEGAKAEQEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAY
SQQMKASRGQFSNFNFNDAPLGTTATDNANSNNSAPSGAGAAFGSNAEEDDDLYS
Sequence of entity 2 (H), FASTA
>6OAB_2 poly(alanine) substrate (chains H)
AAAAAAAAAAAAAAAAAAAAAAAA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| BEF | Beryllium trifluoride ion | Be F3 | 8 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 10 |
Primary citation
Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding. Twomey, E.C., Ji, Z., Wales, T.E. et al. Science (2019) 365. DOI 10.1126/science.aax1033 · 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
- 8DAW 3.6 Å, Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties and…
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