6OAA: Cell division control protein 48
Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 1. Determined by electron microscopy at 4.1 Å resolution. Released 3 Jul 2019.
- Method
- Electron microscopy
- Resolution
- 4.1 Å
- Organisms
- Saccharomyces cerevisiae S288C, Saccharomyces cerevisiae
- Chains
- 6
- Atoms
- 19,546
- Mol. weight
- 446.67 kDa
- Ligands
- ADP, BEF
- Released
- 3 Jul 2019
Explore 6OAA in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6OAA contains 116 α-helices and 78 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 B: 25 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 220-227 | 8 | |
| α-helix | 232-235 | 4 | |
| β-strand | 252-254 | 3 | 1 |
| α-helix | 262-271 | 10 | |
| β-strand | 277-279 | 3 | 1 |
| α-helix | 297-304 | 8 | |
| β-strand | 311-314 | 4 | 1 |
| α-helix | 331-344 | 14 | |
| β-strand | 355-356 | 2 | 1 |
| α-helix | 360-362 | 3 | |
| α-helix | 365-368 | 4 | |
| β-strand | 377-378 | 2 | 1 |
| α-helix | 380-382 | 3 | |
| α-helix | 387-394 | 8 | |
| α-helix | 406-412 | 7 | |
| α-helix | 419-435 | 17 | |
| α-helix | 459-467 | 9 | |
| α-helix | 478-480 | 3 | |
| α-helix | 495-508 | 14 | |
| α-helix | 512-516 | 5 | |
| α-helix | 518-521 | 4 | |
| β-strand | 524-527 | 4 | 2 |
| α-helix | 537-543 | 7 | |
| β-strand | 549-552 | 4 | 2 |
| α-helix | 564-567 | 4 | |
| α-helix | 572-578 | 7 | |
| β-strand | 583-587 | 5 | 2 |
| α-helix | 590-593 | 4 | |
| α-helix | 594-596 | 3 | |
| α-helix | 609-619 | 11 | |
| β-strand | 628-632 | 5 | 2 |
| β-strand | 651-654 | 4 | 2 |
| α-helix | 660-670 | 11 | |
| α-helix | 683-688 | 6 | |
| α-helix | 696-715 | 20 | |
Chain C: 22 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 220-230 | 11 | |
| α-helix | 232-235 | 4 | |
| α-helix | 246-247 | 2 | |
| β-strand | 252-253 | 2 | 3 |
| β-strand | 254 | 1 | 4 |
| β-strand | 275-279 | 5 | 3 |
| α-helix | 294-303 | 10 | |
| β-strand | 309-314 | 6 | 3 |
| α-helix | 331-342 | 12 | |
| β-strand | 352-356 | 5 | 3 |
| α-helix | 365-368 | 4 | |
| β-strand | 378 | 1 | 4 |
| α-helix | 388-393 | 6 | |
| β-strand | 400 | 1 | 5 |
| α-helix | 406-411 | 6 | |
| α-helix | 420-435 | 16 | |
| β-strand | 457 | 1 | 5 |
| α-helix | 461-465 | 5 | |
| α-helix | 493-508 | 16 | |
| α-helix | 510-516 | 7 | |
| α-helix | 519-521 | 3 | |
| β-strand | 524-526 | 3 | 6 |
| α-helix | 538-541 | 4 | |
| β-strand | 548-553 | 6 | 6 |
| α-helix | 564-578 | 15 | |
| β-strand | 582-587 | 6 | 6 |
| α-helix | 609-615 | 7 | |
| α-helix | 616-620 | 5 | |
| β-strand | 627-632 | 6 | 6 |
| β-strand | 651-653 | 3 | 6 |
| α-helix | 662-671 | 10 | |
| α-helix | 683-687 | 5 | |
| α-helix | 696-710 | 15 | |
| α-helix | 755-759 | 5 | |
| α-helix | 771-778 | 8 | |
Chain D: 32 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 221-230 | 10 | |
| α-helix | 232-235 | 4 | |
| α-helix | 246-248 | 3 | |
| β-strand | 250-254 | 5 | 7 |
| α-helix | 264-267 | 4 | |
| β-strand | 279 | 1 | 8 |
| α-helix | 282-284 | 3 | |
| α-helix | 294-301 | 8 | |
| β-strand | 311-312 | 2 | 7 |
| β-strand | 313 | 1 | 8 |
| β-strand | 321 | 1 | 9 |
| α-helix | 329-340 | 12 | |
| β-strand | 353-356 | 4 | 7 |
| β-strand | 363 | 1 | 9 |
| α-helix | 365-367 | 3 | |
| β-strand | 377-378 | 2 | 7 |
| α-helix | 388-391 | 4 | |
| α-helix | 408-411 | 4 | |
| 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 | 524-526 | 3 | 10 |
| β-strand | 527 | 1 | 11 |
| α-helix | 536-544 | 9 | |
| β-strand | 548-552 | 5 | 10 |
| β-strand | 561 | 1 | 12 |
| α-helix | 570-579 | 10 | |
| β-strand | 582-587 | 6 | 10 |
| α-helix | 589-593 | 5 | |
| α-helix | 609-615 | 7 | |
| α-helix | 616-620 | 5 | |
| α-helix | 623-624 | 2 | |
| β-strand | 629-632 | 4 | 10 |
| α-helix | 636-638 | 3 | |
| β-strand | 651 | 1 | 10 |
| α-helix | 653 | 1 | |
| β-strand | 654 | 1 | 11 |
| α-helix | 655-658 | 4 | |
| α-helix | 662-670 | 9 | |
| β-strand | 676 | 1 | 13 |
| α-helix | 683-688 | 6 | |
| α-helix | 694-697 | 4 | |
| α-helix | 702-707 | 6 | |
| α-helix | 713-715 | 3 | |
| β-strand | 753 | 1 | 13 |
| α-helix | 771-777 | 7 | |
Chain E: 20 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 221-226 | 6 | |
| α-helix | 227-231 | 5 | |
| α-helix | 232-235 | 4 | |
| α-helix | 246-248 | 3 | |
| β-strand | 250-254 | 5 | 14 |
| α-helix | 262-272 | 11 | |
| β-strand | 275-276 | 2 | 15 |
| β-strand | 279 | 1 | 14 |
| α-helix | 297-302 | 6 | |
| β-strand | 309-310 | 2 | 15 |
| β-strand | 313-314 | 2 | 14 |
| β-strand | 321 | 1 | 16 |
| α-helix | 329-342 | 14 | |
| β-strand | 353-357 | 5 | 14 |
| β-strand | 363 | 1 | 16 |
| α-helix | 365-367 | 3 | |
| β-strand | 375-378 | 4 | 14 |
| α-helix | 388-394 | 7 | |
| α-helix | 406-412 | 7 | |
| α-helix | 420-435 | 16 | |
| α-helix | 459-467 | 9 | |
| α-helix | 482 | 1 | |
| α-helix | 493-502 | 10 | |
| α-helix | 510-516 | 7 | |
| β-strand | 523-527 | 5 | 17 |
| α-helix | 534-544 | 11 | |
| β-strand | 548-551 | 4 | 17 |
| α-helix | 564-578 | 15 | |
| β-strand | 582-586 | 5 | 17 |
| α-helix | 589-591 | 3 | |
| α-helix | 609-616 | 8 | |
| β-strand | 627-633 | 7 | 17 |
| β-strand | 651-652 | 2 | 17 |
| α-helix | 660-667 | 8 | |
Chain G: 16 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 117-124 | 8 | |
| α-helix | 156-159 | 4 | |
| α-helix | 170-175 | 6 | |
| β-strand | 193 | 1 | 18 |
| α-helix | 200-201 | 2 | |
| α-helix | 217-219 | 3 | |
| β-strand | 224 | 1 | 19 |
| α-helix | 227-229 | 3 | |
| β-strand | 236-238 | 3 | 20 |
| α-helix | 242-255 | 14 | |
| β-strand | 260-270 | 11 | 20 |
| β-strand | 276-285 | 10 | 20 |
| β-strand | 291 | 1 | 21 |
| β-strand | 296 | 1 | 21 |
| α-helix | 301-312 | 12 | |
| β-strand | 320-327 | 8 | 20 |
| α-helix | 352-363 | 12 | |
| α-helix | 366-367 | 2 | |
| β-strand | 368 | 1 | 22 |
| β-strand | 372 | 1 | 18 |
| β-strand | 376 | 1 | 22 |
| β-strand | 382-386 | 5 | 20 |
| β-strand | 396-401 | 6 | 20 |
| β-strand | 414-415 | 2 | 23 |
| β-strand | 422 | 1 | 24 |
| β-strand | 424-425 | 2 | 23 |
| β-strand | 437 | 1 | 19 |
| β-strand | 458 | 1 | 24 |
| β-strand | 463-465 | 3 | 20 |
| β-strand | 467 | 1 | 20 |
| β-strand | 470 | 1 | 25 |
| α-helix | 501-507 | 7 | |
| α-helix | 518-524 | 7 | |
| α-helix | 527-535 | 9 | |
| α-helix | 541-549 | 9 | |
| α-helix | 557-564 | 8 | |
| α-helix | 567-578 | 12 | |
Chain H: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3 | 1 | 12 |
| α-helix | 25-29 | 5 | |
| β-strand | 41 | 1 | 25 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cell division control protein 48 | B, C, D, E | protein | 835 | Saccharomyces cerevisiae S288C | P25694 (AlphaFold model) |
| Nuclear protein localization protein 4 | G | protein | 580 | Saccharomyces cerevisiae | P33755 (AlphaFold model) |
| Ubiquitin | H | protein | 76 | Saccharomyces cerevisiae | P0CH08 (AlphaFold model) |
Sequence of entity 1 (B, C, D, E), FASTA
>6OAA_1 Cell division control protein 48 (chains B, C, D, E)
MGEEHKPLLDASGVDPREEDKTATAILRRKKKDNMLLVDDAINDDNSVIAINSNTMDKLE
LFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKY
ATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEP
EEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLF
KAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAF
EEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRP
NSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGAD
IASLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVE
SVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKA
VATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSL
GDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDE
NARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHE
AEKEVKVEGEDVEMTDEGAKAEQEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAY
SQQMKASRGQFSNFNFNDAPLGTTATDNANSNNSAPSGAGAAFGSNAEEDDDLYS
Sequence of entity 2 (G), FASTA
>6OAA_2 Nuclear protein localization protein 4 (chains G)
MLIRFRSKNGTHRVSCQENDLFGTVIEKLVGNLDPNADVDTFTVCEKPGQGIHAVSELAD
RTVMDLGLKHGDMLILNYSDKPANEKDGVNVEIGSVGIDSKGIRQHRYGPLRIKELAVDE
ELEKEDGLIPRQKSKLCKHGDRGMCEYCSPLPPWDKEYHEKNKIKHISFHSYLKKLNENA
NKKENGSSYISPLSEPDFRINKRCHNGHEPWPRGICSKCQPSAITLQQQEFRMVDHVEFQ
KSEIINEFIQAWRYTGMQRFGYMYGSYSKYDNTPLGIKAVVEAIYEPPQHDEQDGLTMDV
EQVKNEMLQIDRQAQEMGLSRIGLIFTDLSDAGAGDGSVFCKRHKDSFFLSSLEVIMAAR
HQTRHPNVSKYSEQGFFSSKFVTCVISGNLEGEIDISSYQVSTEAEALVTADMISGSTFP
SMAYINDTTDERYVPEIFYMKSNEYGITVKENAKPAFPVDYLLVTLTHGFPNTDTETNSK
FVSSTGFPWSNRQAMGQSQDYQELKKYLFNVASSGDFNLLHEKISNFHLLLYINSLQILS
PDEWKLLIESAVKNEWEESLLKLVSSAGWQTLVMILQESG
Sequence of entity 3 (H), FASTA
>6OAA_3 Ubiquitin (chains H)
MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 8 |
| BEF | Beryllium trifluoride ion | Be F3 | 6 |
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
- 6OAB 3.6 Å, Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx,…
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