8UB4: Cell division control protein 48
Cdc48-Shp1 unfolding native substrate, consensus structure. Determined by electron microscopy at 2.9 Å resolution. Released 6 Nov 2024.
- Method
- Electron microscopy
- Resolution
- 2.9 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 10
- Atoms
- 23,006
- Mol. weight
- 700.45 kDa
- Ligands
- ADP, MG, 08T
- Released
- 6 Nov 2024
Explore 8UB4 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8UB4 contains 182 α-helices and 96 β-strands across 10 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: 33 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 213-215 | 3 | |
| α-helix | 220-230 | 11 | |
| α-helix | 232-235 | 4 | |
| α-helix | 238-243 | 6 | |
| α-helix | 246-248 | 3 | |
| β-strand | 251-254 | 4 | 1 |
| α-helix | 261-271 | 11 | |
| β-strand | 276-280 | 5 | 1 |
| α-helix | 281-283 | 3 | |
| α-helix | 292-306 | 15 | |
| β-strand | 310-314 | 5 | 1 |
| α-helix | 316-319 | 4 | |
| α-helix | 323-325 | 3 | |
| α-helix | 330-343 | 14 | |
| β-strand | 352-356 | 5 | 1 |
| α-helix | 360-362 | 3 | |
| α-helix | 365-368 | 4 | |
| β-strand | 375-378 | 4 | 1 |
| α-helix | 384-395 | 12 | |
| β-strand | 400 | 1 | 2 |
| α-helix | 406-412 | 7 | |
| α-helix | 419-435 | 17 | |
| α-helix | 450-453 | 4 | |
| β-strand | 457 | 1 | 2 |
| α-helix | 459-467 | 9 | |
| α-helix | 472-474 | 3 | |
| α-helix | 493-508 | 16 | |
| α-helix | 510-516 | 7 | |
| α-helix | 519-521 | 3 | |
| β-strand | 523-527 | 5 | 3 |
| α-helix | 534-543 | 10 | |
| β-strand | 550-553 | 4 | 3 |
| α-helix | 554-557 | 4 | |
| α-helix | 564-578 | 15 | |
| β-strand | 582-587 | 6 | 3 |
| β-strand | 594 | 1 | 4 |
| α-helix | 606-618 | 13 | |
| β-strand | 627-633 | 7 | 3 |
| β-strand | 639 | 1 | 4 |
| α-helix | 641-644 | 4 | |
| β-strand | 651-654 | 4 | 3 |
| α-helix | 660-670 | 11 | |
| β-strand | 676 | 1 | 5 |
| α-helix | 683-688 | 6 | |
| α-helix | 694-723 | 30 | |
| β-strand | 753 | 1 | 5 |
| α-helix | 755-761 | 7 | |
| α-helix | 762-764 | 3 | |
| α-helix | 771-783 | 13 | |
Chain B: 34 helices, 16 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 | 6 |
| α-helix | 261-271 | 11 | |
| β-strand | 275-280 | 6 | 6 |
| α-helix | 282-284 | 3 | |
| β-strand | 288 | 1 | 7 |
| α-helix | 292-306 | 15 | |
| β-strand | 309-314 | 6 | 6 |
| α-helix | 316-319 | 4 | |
| α-helix | 330-342 | 13 | |
| β-strand | 351-357 | 7 | 6 |
| α-helix | 360-362 | 3 | |
| α-helix | 365-368 | 4 | |
| β-strand | 375-378 | 4 | 6 |
| α-helix | 384-394 | 11 | |
| α-helix | 406-412 | 7 | |
| α-helix | 419-433 | 15 | |
| α-helix | 449-452 | 4 | |
| α-helix | 459-467 | 9 | |
| α-helix | 472-474 | 3 | |
| α-helix | 478-480 | 3 | |
| α-helix | 486-488 | 3 | |
| α-helix | 493-508 | 16 | |
| α-helix | 510-516 | 7 | |
| α-helix | 519-521 | 3 | |
| β-strand | 524-527 | 4 | 8 |
| α-helix | 534-544 | 11 | |
| β-strand | 548-552 | 5 | 8 |
| α-helix | 555-557 | 3 | |
| β-strand | 561 | 1 | 9 |
| α-helix | 564-578 | 15 | |
| β-strand | 582-587 | 6 | 8 |
| β-strand | 594 | 1 | 10 |
| α-helix | 595 | 1 | |
| α-helix | 606-618 | 13 | |
| β-strand | 627-633 | 7 | 8 |
| β-strand | 639 | 1 | 10 |
| α-helix | 641-644 | 4 | |
| β-strand | 651-654 | 4 | 8 |
| α-helix | 660-670 | 11 | |
| β-strand | 676 | 1 | 11 |
| α-helix | 683-689 | 7 | |
| α-helix | 694-721 | 28 | |
| β-strand | 753 | 1 | 11 |
| α-helix | 755-759 | 5 | |
| α-helix | 771-785 | 15 | |
| α-helix | 786-788 | 3 | |
Chain C: 30 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 213-215 | 3 | |
| α-helix | 220-235 | 16 | |
| α-helix | 238-243 | 6 | |
| α-helix | 246-248 | 3 | |
| β-strand | 250-254 | 5 | 12 |
| α-helix | 261-271 | 11 | |
| β-strand | 275-279 | 5 | 12 |
| α-helix | 281-283 | 3 | |
| α-helix | 292-306 | 15 | |
| β-strand | 309-314 | 6 | 12 |
| α-helix | 316-319 | 4 | |
| α-helix | 330-342 | 13 | |
| β-strand | 352-357 | 6 | 12 |
| α-helix | 365-367 | 3 | |
| β-strand | 375-378 | 4 | 12 |
| α-helix | 384-394 | 11 | |
| α-helix | 406-412 | 7 | |
| α-helix | 419-439 | 21 | |
| α-helix | 449-452 | 4 | |
| α-helix | 459-467 | 9 | |
| α-helix | 472-474 | 3 | |
| α-helix | 478-480 | 3 | |
| α-helix | 493-508 | 16 | |
| α-helix | 510-516 | 7 | |
| α-helix | 519-521 | 3 | |
| β-strand | 524-527 | 4 | 13 |
| α-helix | 534-544 | 11 | |
| β-strand | 548-552 | 5 | 13 |
| β-strand | 561 | 1 | 14 |
| α-helix | 564-578 | 15 | |
| β-strand | 582-587 | 6 | 13 |
| α-helix | 589-592 | 4 | |
| α-helix | 607-618 | 12 | |
| β-strand | 627-633 | 7 | 13 |
| α-helix | 636-638 | 3 | |
| β-strand | 651-654 | 4 | 13 |
| α-helix | 660-670 | 11 | |
| β-strand | 676 | 1 | 15 |
| α-helix | 683-689 | 7 | |
| α-helix | 694-721 | 28 | |
| β-strand | 753 | 1 | 15 |
| α-helix | 755-761 | 7 | |
| α-helix | 771-786 | 16 | |
Chain D: 33 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 213-215 | 3 | |
| α-helix | 220-235 | 16 | |
| α-helix | 238-243 | 6 | |
| α-helix | 246-248 | 3 | |
| β-strand | 250-254 | 5 | 16 |
| α-helix | 261-271 | 11 | |
| β-strand | 275-280 | 6 | 16 |
| α-helix | 282-284 | 3 | |
| α-helix | 292-305 | 14 | |
| β-strand | 309-314 | 6 | 16 |
| α-helix | 316-319 | 4 | |
| α-helix | 329-342 | 14 | |
| β-strand | 351-357 | 7 | 16 |
| α-helix | 360-362 | 3 | |
| α-helix | 365-367 | 3 | |
| β-strand | 375 | 1 | 16 |
| β-strand | 378 | 1 | 16 |
| α-helix | 384-394 | 11 | |
| α-helix | 407-412 | 6 | |
| α-helix | 419-435 | 17 | |
| α-helix | 449-452 | 4 | |
| α-helix | 459-467 | 9 | |
| α-helix | 472-475 | 4 | |
| α-helix | 478-480 | 3 | |
| α-helix | 486-488 | 3 | |
| α-helix | 493-508 | 16 | |
| α-helix | 510-516 | 7 | |
| α-helix | 519-521 | 3 | |
| β-strand | 524-527 | 4 | 17 |
| α-helix | 534-543 | 10 | |
| β-strand | 548-552 | 5 | 17 |
| β-strand | 561 | 1 | 18 |
| α-helix | 565-578 | 14 | |
| β-strand | 582-587 | 6 | 17 |
| α-helix | 589-592 | 4 | |
| α-helix | 594-596 | 3 | |
| α-helix | 602-618 | 17 | |
| β-strand | 627-633 | 7 | 17 |
| α-helix | 636-638 | 3 | |
| β-strand | 651-654 | 4 | 17 |
| α-helix | 660-670 | 11 | |
| β-strand | 676 | 1 | 19 |
| α-helix | 682-687 | 6 | |
| α-helix | 694-721 | 28 | |
| β-strand | 753 | 1 | 19 |
| α-helix | 755-762 | 8 | |
| α-helix | 771-786 | 16 | |
Chain E: 26 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 213-215 | 3 | |
| α-helix | 220-235 | 16 | |
| α-helix | 237-243 | 7 | |
| β-strand | 251-254 | 4 | 20 |
| α-helix | 261-271 | 11 | |
| β-strand | 275-280 | 6 | 20 |
| α-helix | 281-284 | 4 | |
| α-helix | 292-305 | 14 | |
| β-strand | 309-314 | 6 | 20 |
| α-helix | 316-319 | 4 | |
| α-helix | 330-342 | 13 | |
| β-strand | 351-357 | 7 | 20 |
| β-strand | 375 | 1 | 20 |
| β-strand | 378 | 1 | 20 |
| α-helix | 384-397 | 14 | |
| β-strand | 400 | 1 | 21 |
| α-helix | 406-412 | 7 | |
| α-helix | 419-435 | 17 | |
| β-strand | 457 | 1 | 21 |
| α-helix | 459-467 | 9 | |
| α-helix | 493-508 | 16 | |
| α-helix | 510-516 | 7 | |
| α-helix | 519-521 | 3 | |
| β-strand | 524-527 | 4 | 22 |
| α-helix | 534-544 | 11 | |
| β-strand | 548-553 | 6 | 22 |
| α-helix | 555-557 | 3 | |
| β-strand | 561 | 1 | 23 |
| α-helix | 564-578 | 15 | |
| β-strand | 582-587 | 6 | 22 |
| α-helix | 589-592 | 4 | |
| β-strand | 594 | 1 | 24 |
| α-helix | 602-618 | 17 | |
| β-strand | 628-633 | 6 | 22 |
| α-helix | 636-638 | 3 | |
| β-strand | 639 | 1 | 24 |
| β-strand | 651-654 | 4 | 22 |
| α-helix | 660-670 | 11 | |
| α-helix | 683-686 | 4 | |
| α-helix | 694-710 | 17 | |
| α-helix | 755-761 | 7 | |
| α-helix | 771-784 | 14 | |
Chain F: 23 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 220-235 | 16 | |
| α-helix | 237-243 | 7 | |
| β-strand | 250-254 | 5 | 25 |
| α-helix | 261-271 | 11 | |
| β-strand | 276 | 1 | 25 |
| β-strand | 279-280 | 2 | 25 |
| α-helix | 291-306 | 16 | |
| β-strand | 310-314 | 5 | 25 |
| α-helix | 316-318 | 3 | |
| α-helix | 330-343 | 14 | |
| β-strand | 352-356 | 5 | 25 |
| β-strand | 375-378 | 4 | 25 |
| α-helix | 384-395 | 12 | |
| α-helix | 406-412 | 7 | |
| α-helix | 419-435 | 17 | |
| α-helix | 459-467 | 9 | |
| α-helix | 493-507 | 15 | |
| β-strand | 524-527 | 4 | 26 |
| α-helix | 534-543 | 10 | |
| β-strand | 550-552 | 3 | 26 |
| α-helix | 564-566 | 3 | |
| α-helix | 568-578 | 11 | |
| β-strand | 584-587 | 4 | 26 |
| α-helix | 589-593 | 5 | |
| α-helix | 602-618 | 17 | |
| α-helix | 624-626 | 3 | |
| β-strand | 629-633 | 5 | 26 |
| α-helix | 636-638 | 3 | |
| β-strand | 653-654 | 2 | 26 |
| α-helix | 660-670 | 11 | |
| β-strand | 676 | 1 | 27 |
| α-helix | 683-688 | 6 | |
| α-helix | 694-724 | 31 | |
| β-strand | 753 | 1 | 27 |
| α-helix | 755-761 | 7 | |
| α-helix | 762-764 | 3 | |
Chain G: 0 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3 | 1 | 7 |
| β-strand | 15 | 1 | 9 |
| β-strand | 17 | 1 | 14 |
| β-strand | 19 | 1 | 18 |
| β-strand | 21 | 1 | 23 |
Chains H and I: 1 helix, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 6 |
| α-helix | 5-14 | 10 | |
1 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 | 835 | Saccharomyces cerevisiae | P25694 (AlphaFold model) |
| Substrate | G | protein | 22 | Saccharomyces cerevisiae | |
| UBX domain-containing protein 1 | H, I, J | protein | 423 | Saccharomyces cerevisiae | P34223 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F), FASTA
>8UB4_1 Cell division control protein 48 (chains A, B, C, D, E, F)
MGEEHKPLLDASGVDPREEDKTATAILRRKKKDNMLLVDDAINDDNSVIAINSNTMDKLE
LFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKY
ATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEP
EEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLF
KAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAF
EEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRP
NSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGAD
IASLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVE
SVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKA
VATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSL
GDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDE
NARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHE
AEKEVKVEGEDVEMTDEGAKAEQEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAY
SQQMKASRGQFSNFNFNDAPLGTTATDNANSNNSAPSGAGAAFGSNAEEDDDLYS
Sequence of entity 2 (G), FASTA
>8UB4_2 Substrate (chains G)
AAAAAAAAAAAAAVAVAVAVAA
Sequence of entity 3 (H, I, J), FASTA
>8UB4_3 UBX domain-containing protein 1 (chains H, I, J)
MAEIPDETIQQFMALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQKDRREEAHWNRQ
QEKALKQEAFSTNSSNKAINTEHVGGLCPKPGSSQGSNEYLKRKGSTSPEPTKGSSRSGS
GNNSRFMSFSDMVRGQADDDDEDQPRNTFAGGETSGLEVTDPSDPNSLLKDLLEKARRGG
QMGAENGFRDDEDHEMGANRFTGRGFRLGSTIDAADEVVEDNTSQSQRRPEKVTREITFW
KEGFQVADGPLYRYDDPANSFYLSELNQGRAPLKLLDVQFGQEVEVNVYKKLDESYKAPT
RKLGGFSGQGQRLGSPIPGESSPAEVPKNETPAAQEQPMPDNEPKQGDTSIQIRYANGKR
EVLHCNSTDTVKFLYEHVTSNANTDPSRNFTLNYAFPIKPISNDETTLKDADLLNSVVVQ
RWA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 2 |
| MG | Magnesium ion | Mg | 8 |
| 08T | [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxi… | C10 H14 Be F3 N5 O10 P2 | 8 |
Primary citation
Visualization of the Cdc48 AAA+ ATPase protein unfolding pathway. Cooney, I., Schubert, H.L., Cedeno, K. et al. Nat Commun (2024) 15:7505-7505. DOI 10.1038/s41467-024-51835-3 · PubMed
Other PDB entries of the same protein (UniProt P25694 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 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,…
- 8DAW 3.6 Å, Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties and…
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