8U9Z: Cdc48-Shp1 unfolding native substrate, Class 7
Cdc48-Shp1 unfolding native substrate, Class 7. Determined by electron microscopy at 3.8 Å resolution. Released 6 Nov 2024.
- Method
- Electron microscopy
- Resolution
- 3.8 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 7
- Atoms
- 22,973
- Mol. weight
- 558.29 kDa
- Ligands
- ADP, MG, 08T
- Released
- 6 Nov 2024
Explore 8U9Z in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8U9Z contains 179 α-helices and 82 β-strands across 7 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: 31 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 220-235 | 16 | |
| α-helix | 237-243 | 7 | |
| α-helix | 246-248 | 3 | |
| β-strand | 250-254 | 5 | 1 |
| α-helix | 261-271 | 11 | |
| β-strand | 276-280 | 5 | 1 |
| α-helix | 281-283 | 3 | |
| α-helix | 291-306 | 16 | |
| β-strand | 310-314 | 5 | 1 |
| α-helix | 316-319 | 4 | |
| α-helix | 330-344 | 15 | |
| 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 | 420-440 | 21 | |
| α-helix | 452-454 | 3 | |
| β-strand | 457 | 1 | 2 |
| α-helix | 459-468 | 10 | |
| α-helix | 472-475 | 4 | |
| α-helix | 493-508 | 16 | |
| α-helix | 510-516 | 7 | |
| β-strand | 524-527 | 4 | 3 |
| α-helix | 534-544 | 11 | |
| β-strand | 550-553 | 4 | 3 |
| α-helix | 554-556 | 3 | |
| β-strand | 561 | 1 | 4 |
| α-helix | 564-578 | 15 | |
| β-strand | 582-587 | 6 | 3 |
| α-helix | 589-591 | 3 | |
| α-helix | 606-618 | 13 | |
| β-strand | 627-633 | 7 | 3 |
| α-helix | 636-638 | 3 | |
| α-helix | 641-644 | 4 | |
| β-strand | 651-654 | 4 | 3 |
| α-helix | 656-658 | 3 | |
| α-helix | 660-670 | 11 | |
| α-helix | 683-688 | 6 | |
| α-helix | 694-724 | 31 | |
| α-helix | 755-763 | 9 | |
| α-helix | 771-783 | 13 | |
Chain B: 32 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 206-209 | 4 | |
| α-helix | 220-235 | 16 | |
| α-helix | 237-243 | 7 | |
| α-helix | 246-248 | 3 | |
| β-strand | 250-254 | 5 | 5 |
| α-helix | 261-271 | 11 | |
| β-strand | 275-280 | 6 | 5 |
| α-helix | 282-284 | 3 | |
| β-strand | 288 | 1 | 6 |
| α-helix | 292-305 | 14 | |
| β-strand | 309-314 | 6 | 5 |
| α-helix | 316-318 | 3 | |
| α-helix | 330-342 | 13 | |
| β-strand | 351-357 | 7 | 5 |
| α-helix | 360-362 | 3 | |
| α-helix | 365-368 | 4 | |
| β-strand | 375-378 | 4 | 5 |
| α-helix | 384-394 | 11 | |
| β-strand | 400 | 1 | 7 |
| α-helix | 406-412 | 7 | |
| α-helix | 419-436 | 18 | |
| α-helix | 449-452 | 4 | |
| β-strand | 457 | 1 | 7 |
| α-helix | 459-468 | 10 | |
| α-helix | 474-477 | 4 | |
| 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 |
| α-helix | 589-592 | 4 | |
| α-helix | 606-618 | 13 | |
| β-strand | 627-633 | 7 | 8 |
| β-strand | 652-654 | 3 | 8 |
| α-helix | 656-658 | 3 | |
| α-helix | 660-670 | 11 | |
| β-strand | 676 | 1 | 10 |
| α-helix | 683-688 | 6 | |
| α-helix | 694-721 | 28 | |
| β-strand | 753 | 1 | 10 |
| α-helix | 755-761 | 7 | |
| α-helix | 771-787 | 17 | |
Chain C: 32 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 202-209 | 8 | |
| α-helix | 214-216 | 3 | |
| α-helix | 220-235 | 16 | |
| α-helix | 238-243 | 6 | |
| α-helix | 246-248 | 3 | |
| β-strand | 250-254 | 5 | 11 |
| α-helix | 261-271 | 11 | |
| β-strand | 276-279 | 4 | 11 |
| α-helix | 282-284 | 3 | |
| α-helix | 292-306 | 15 | |
| β-strand | 310-314 | 5 | 11 |
| α-helix | 316-318 | 3 | |
| α-helix | 330-342 | 13 | |
| β-strand | 352-357 | 6 | 11 |
| α-helix | 365-367 | 3 | |
| β-strand | 375-378 | 4 | 11 |
| α-helix | 384-394 | 11 | |
| α-helix | 407-412 | 6 | |
| α-helix | 419-439 | 21 | |
| α-helix | 459-468 | 10 | |
| α-helix | 473-477 | 5 | |
| 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 | 12 |
| α-helix | 534-544 | 11 | |
| β-strand | 548-552 | 5 | 12 |
| β-strand | 561 | 1 | 13 |
| α-helix | 564-578 | 15 | |
| β-strand | 582-587 | 6 | 12 |
| α-helix | 589-592 | 4 | |
| α-helix | 606-618 | 13 | |
| β-strand | 627-633 | 7 | 12 |
| α-helix | 636-638 | 3 | |
| α-helix | 641-644 | 4 | |
| β-strand | 651-654 | 4 | 12 |
| α-helix | 660-670 | 11 | |
| α-helix | 683-688 | 6 | |
| α-helix | 694-721 | 28 | |
| α-helix | 755-761 | 7 | |
| α-helix | 762-764 | 3 | |
| α-helix | 771-788 | 18 | |
Chain D: 33 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 220-235 | 16 | |
| α-helix | 238-243 | 6 | |
| α-helix | 245-248 | 4 | |
| β-strand | 251-254 | 4 | 14 |
| α-helix | 261-271 | 11 | |
| β-strand | 275-279 | 5 | 14 |
| α-helix | 292-306 | 15 | |
| β-strand | 309-314 | 6 | 14 |
| α-helix | 316-318 | 3 | |
| α-helix | 329-342 | 14 | |
| β-strand | 352-357 | 6 | 14 |
| α-helix | 365-368 | 4 | |
| β-strand | 375 | 1 | 14 |
| β-strand | 378 | 1 | 14 |
| α-helix | 381-383 | 3 | |
| α-helix | 384-394 | 11 | |
| α-helix | 395-397 | 3 | |
| β-strand | 400 | 1 | 15 |
| α-helix | 406-412 | 7 | |
| α-helix | 419-437 | 19 | |
| α-helix | 450-453 | 4 | |
| β-strand | 457 | 1 | 15 |
| α-helix | 459-468 | 10 | |
| α-helix | 486-488 | 3 | |
| α-helix | 493-508 | 16 | |
| α-helix | 510-516 | 7 | |
| α-helix | 519-521 | 3 | |
| β-strand | 523-527 | 5 | 16 |
| α-helix | 534-544 | 11 | |
| β-strand | 548-552 | 5 | 16 |
| α-helix | 554-557 | 4 | |
| β-strand | 561 | 1 | 17 |
| α-helix | 565-578 | 14 | |
| β-strand | 582-587 | 6 | 16 |
| α-helix | 589-592 | 4 | |
| α-helix | 601-618 | 18 | |
| β-strand | 627-633 | 7 | 16 |
| α-helix | 636-638 | 3 | |
| α-helix | 641-644 | 4 | |
| β-strand | 651-654 | 4 | 16 |
| α-helix | 655-658 | 4 | |
| α-helix | 660-671 | 12 | |
| α-helix | 683-688 | 6 | |
| α-helix | 694-713 | 20 | |
| α-helix | 755-762 | 8 | |
| α-helix | 772-787 | 16 | |
| α-helix | 790-792 | 3 | |
Chain E: 24 helices, 10 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 | 18 |
| α-helix | 261-271 | 11 | |
| β-strand | 276-279 | 4 | 18 |
| α-helix | 281-284 | 4 | |
| α-helix | 292-305 | 14 | |
| β-strand | 310-314 | 5 | 18 |
| α-helix | 316-319 | 4 | |
| α-helix | 329-342 | 14 | |
| β-strand | 352-357 | 6 | 18 |
| β-strand | 375-378 | 4 | 18 |
| α-helix | 384-394 | 11 | |
| α-helix | 406-412 | 7 | |
| α-helix | 419-435 | 17 | |
| α-helix | 459-467 | 9 | |
| α-helix | 493-508 | 16 | |
| α-helix | 510-516 | 7 | |
| β-strand | 524-527 | 4 | 19 |
| α-helix | 534-542 | 9 | |
| β-strand | 548-552 | 5 | 19 |
| α-helix | 564-577 | 14 | |
| β-strand | 582-587 | 6 | 19 |
| α-helix | 589-592 | 4 | |
| α-helix | 602-618 | 17 | |
| β-strand | 628-632 | 5 | 19 |
| α-helix | 636-638 | 3 | |
| β-strand | 651-654 | 4 | 19 |
| α-helix | 660-670 | 11 | |
| α-helix | 682-687 | 6 | |
| α-helix | 694-712 | 19 | |
| α-helix | 755-761 | 7 | |
Chain F: 25 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 222-235 | 14 | |
| α-helix | 237-243 | 7 | |
| β-strand | 251-254 | 4 | 20 |
| α-helix | 261-271 | 11 | |
| β-strand | 276-280 | 5 | 20 |
| α-helix | 282-284 | 3 | |
| α-helix | 291-306 | 16 | |
| β-strand | 310-314 | 5 | 20 |
| α-helix | 316-319 | 4 | |
| α-helix | 330-342 | 13 | |
| β-strand | 352-356 | 5 | 20 |
| β-strand | 376-378 | 3 | 20 |
| α-helix | 384-394 | 11 | |
| α-helix | 395-397 | 3 | |
| α-helix | 406-412 | 7 | |
| α-helix | 420-435 | 16 | |
| α-helix | 450-453 | 4 | |
| α-helix | 459-467 | 9 | |
| α-helix | 493-507 | 15 | |
| β-strand | 524-525 | 2 | 21 |
| β-strand | 526-527 | 2 | 22 |
| α-helix | 534-543 | 10 | |
| β-strand | 550-552 | 3 | 21 |
| α-helix | 555-557 | 3 | |
| α-helix | 564-578 | 15 | |
| β-strand | 583-587 | 5 | 21 |
| α-helix | 589-593 | 5 | |
| α-helix | 606-616 | 11 | |
| β-strand | 628-632 | 5 | 21 |
| β-strand | 653-654 | 2 | 22 |
| α-helix | 660-670 | 11 | |
| β-strand | 676 | 1 | 23 |
| α-helix | 683-688 | 6 | |
| α-helix | 694-718 | 25 | |
| β-strand | 753 | 1 | 23 |
| α-helix | 755-761 | 7 | |
| α-helix | 762-764 | 3 | |
| α-helix | 771-779 | 9 | |
Chain G: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2 | 1 | |
| β-strand | 3 | 1 | 6 |
| α-helix | 4 | 1 | |
| β-strand | 13 | 1 | 4 |
| β-strand | 15 | 1 | 9 |
| β-strand | 17 | 1 | 13 |
| β-strand | 19 | 1 | 17 |
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 | |
Sequence of entity 1 (A, B, C, D, E, F), FASTA
>8U9Z_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
>8U9Z_2 Substrate (chains G)
AAAAAAAAAAAAAVAVAVAVAA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 2 |
| MG | Magnesium ion | Mg | 6 |
| 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 | 6 |
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:
- 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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