6OMB: Cdc48 Hexamer (Subunits A to E) with substrate
Cdc48 Hexamer (Subunits A to E) with substrate bound to the central pore. Determined by electron microscopy at 3.7 Å resolution. Released 17 Jul 2019.
- Method
- Electron microscopy
- Resolution
- 3.7 Å
- Organisms
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Saccharomyces cerevisiae S288C
- Chains
- 6
- Atoms
- 21,815
- Mol. weight
- 467.42 kDa
- Ligands
- MG, BEF, ADP
- Released
- 17 Jul 2019
Explore 6OMB in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6OMB contains 129 α-helices and 74 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: 26 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 220-235 | 16 | |
| α-helix | 238-243 | 6 | |
| α-helix | 246-248 | 3 | |
| β-strand | 251-254 | 4 | 1 |
| α-helix | 261-270 | 10 | |
| β-strand | 276-280 | 5 | 1 |
| α-helix | 292-305 | 14 | |
| β-strand | 310-314 | 5 | 1 |
| α-helix | 330-343 | 14 | |
| β-strand | 352-356 | 5 | 1 |
| β-strand | 375-378 | 4 | 1 |
| α-helix | 384-394 | 11 | |
| α-helix | 395-397 | 3 | |
| α-helix | 406-412 | 7 | |
| α-helix | 420-435 | 16 | |
| α-helix | 459-467 | 9 | |
| α-helix | 478-481 | 4 | |
| α-helix | 493-508 | 16 | |
| α-helix | 510-516 | 7 | |
| α-helix | 519-521 | 3 | |
| β-strand | 523-527 | 5 | 2 |
| α-helix | 534-543 | 10 | |
| β-strand | 550-552 | 3 | 2 |
| α-helix | 555-557 | 3 | |
| β-strand | 561 | 1 | 3 |
| α-helix | 564-578 | 15 | |
| β-strand | 583-587 | 5 | 2 |
| β-strand | 594 | 1 | 4 |
| α-helix | 606-618 | 13 | |
| β-strand | 628-632 | 5 | 2 |
| α-helix | 636-638 | 3 | |
| β-strand | 639 | 1 | 4 |
| β-strand | 653-654 | 2 | 2 |
| α-helix | 660-670 | 11 | |
| β-strand | 676 | 1 | 5 |
| α-helix | 683-688 | 6 | |
| α-helix | 694-724 | 31 | |
| β-strand | 753 | 1 | 5 |
| α-helix | 755-761 | 7 | |
| α-helix | 762-764 | 3 | |
| α-helix | 771-783 | 13 | |
Chain B: 26 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 220-235 | 16 | |
| α-helix | 238-243 | 6 | |
| α-helix | 246-248 | 3 | |
| β-strand | 251-254 | 4 | 6 |
| α-helix | 261-271 | 11 | |
| β-strand | 276-279 | 4 | 6 |
| α-helix | 282-284 | 3 | |
| α-helix | 292-305 | 14 | |
| β-strand | 310-314 | 5 | 6 |
| α-helix | 316-318 | 3 | |
| α-helix | 330-342 | 13 | |
| β-strand | 352-357 | 6 | 6 |
| β-strand | 375-378 | 4 | 6 |
| α-helix | 384-394 | 11 | |
| α-helix | 406-412 | 7 | |
| α-helix | 419-435 | 17 | |
| α-helix | 449-452 | 4 | |
| α-helix | 459-467 | 9 | |
| α-helix | 478-480 | 3 | |
| α-helix | 493-504 | 12 | |
| α-helix | 510-515 | 6 | |
| α-helix | 519-521 | 3 | |
| β-strand | 524-527 | 4 | 7 |
| α-helix | 534-544 | 11 | |
| β-strand | 548-552 | 5 | 7 |
| α-helix | 555-557 | 3 | |
| β-strand | 561 | 1 | 8 |
| α-helix | 564-578 | 15 | |
| β-strand | 582-587 | 6 | 7 |
| α-helix | 607-618 | 12 | |
| β-strand | 627-633 | 7 | 7 |
| β-strand | 651-654 | 4 | 7 |
| α-helix | 660-670 | 11 | |
| β-strand | 676 | 1 | 9 |
| α-helix | 683-688 | 6 | |
| α-helix | 694-721 | 28 | |
| β-strand | 753 | 1 | 9 |
| α-helix | 755-761 | 7 | |
| α-helix | 771-786 | 16 | |
Chain C: 26 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 220-235 | 16 | |
| α-helix | 238-243 | 6 | |
| α-helix | 245-248 | 4 | |
| β-strand | 250-253 | 4 | 10 |
| β-strand | 254 | 1 | 11 |
| α-helix | 261-271 | 11 | |
| β-strand | 275-279 | 5 | 10 |
| α-helix | 281-283 | 3 | |
| α-helix | 292-306 | 15 | |
| β-strand | 309-314 | 6 | 10 |
| α-helix | 330-342 | 13 | |
| β-strand | 352-356 | 5 | 10 |
| β-strand | 375 | 1 | 10 |
| β-strand | 378 | 1 | 11 |
| α-helix | 384-394 | 11 | |
| α-helix | 407-412 | 6 | |
| α-helix | 420-439 | 20 | |
| α-helix | 459-467 | 9 | |
| 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 | 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 | 607-618 | 12 | |
| β-strand | 627-633 | 7 | 12 |
| α-helix | 636-638 | 3 | |
| β-strand | 651-654 | 4 | 12 |
| α-helix | 660-670 | 11 | |
| β-strand | 676 | 1 | 14 |
| α-helix | 683-689 | 7 | |
| α-helix | 694-721 | 28 | |
| β-strand | 753 | 1 | 14 |
| α-helix | 755-761 | 7 | |
| α-helix | 773-786 | 14 | |
Chain D: 28 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 220-235 | 16 | |
| α-helix | 238-243 | 6 | |
| α-helix | 246-248 | 3 | |
| β-strand | 250-253 | 4 | 15 |
| β-strand | 254 | 1 | 16 |
| α-helix | 261-271 | 11 | |
| β-strand | 275-279 | 5 | 15 |
| β-strand | 288 | 1 | 17 |
| α-helix | 292-305 | 14 | |
| β-strand | 309-314 | 6 | 15 |
| α-helix | 316-318 | 3 | |
| α-helix | 329-342 | 14 | |
| β-strand | 352-356 | 5 | 15 |
| β-strand | 375 | 1 | 15 |
| 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 | 478-480 | 3 | |
| α-helix | 486-488 | 3 | |
| α-helix | 493-504 | 12 | |
| α-helix | 510-516 | 7 | |
| α-helix | 519-521 | 3 | |
| β-strand | 524-527 | 4 | 18 |
| α-helix | 534-544 | 11 | |
| β-strand | 548-552 | 5 | 18 |
| α-helix | 555-557 | 3 | |
| β-strand | 561 | 1 | 19 |
| α-helix | 564-578 | 15 | |
| β-strand | 582-587 | 6 | 18 |
| α-helix | 589-592 | 4 | |
| α-helix | 602-618 | 17 | |
| β-strand | 627-633 | 7 | 18 |
| α-helix | 636-638 | 3 | |
| β-strand | 651-654 | 4 | 18 |
| α-helix | 660-670 | 11 | |
| β-strand | 676 | 1 | 20 |
| α-helix | 683-687 | 5 | |
| α-helix | 694-721 | 28 | |
| β-strand | 753 | 1 | 20 |
| α-helix | 755-762 | 8 | |
| α-helix | 773-786 | 14 | |
Chain E: 23 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 220-235 | 16 | |
| α-helix | 238-243 | 6 | |
| α-helix | 246-248 | 3 | |
| β-strand | 250-254 | 5 | 21 |
| α-helix | 261-271 | 11 | |
| β-strand | 276-279 | 4 | 21 |
| α-helix | 281-284 | 4 | |
| α-helix | 292-305 | 14 | |
| β-strand | 310-314 | 5 | 21 |
| α-helix | 329-342 | 14 | |
| β-strand | 352-357 | 6 | 21 |
| β-strand | 375-378 | 4 | 21 |
| 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 | 22 |
| α-helix | 534-542 | 9 | |
| β-strand | 548-552 | 5 | 22 |
| α-helix | 564-577 | 14 | |
| β-strand | 582-587 | 6 | 22 |
| α-helix | 589-592 | 4 | |
| α-helix | 602-618 | 17 | |
| β-strand | 628-632 | 5 | 22 |
| α-helix | 636-638 | 3 | |
| β-strand | 651-654 | 4 | 22 |
| α-helix | 660-670 | 11 | |
| α-helix | 682-687 | 6 | |
| α-helix | 694-712 | 19 | |
| α-helix | 755-761 | 7 | |
| α-helix | 772-787 | 16 | |
Chain G: 0 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7 | 1 | 17 |
| β-strand | 13 | 1 | 3 |
| β-strand | 15 | 1 | 8 |
| β-strand | 17 | 1 | 13 |
| β-strand | 19 | 1 | 19 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cell division control protein 48 | A, B, C, D, E | protein | 835 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P25694 (AlphaFold model) |
| Substrate of Cdc48 | G | protein | 22 | Saccharomyces cerevisiae S288C | |
Sequence of entity 1 (A, B, C, D, E), FASTA
>6OMB_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 (G), FASTA
>6OMB_2 Substrate of Cdc48 (chains G)
XXXXXXXXXXXXXXXXXXXXXX
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 8 |
| BEF | Beryllium trifluoride ion | Be F3 | 8 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 10 |
Primary citation
Structure of the Cdc48 segregase in the act of unfolding an authentic substrate. Cooney, I., Han, H., Stewart, M.G. et al. Science (2019) 365:502-505. DOI 10.1126/science.aax0486 · 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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