6OA9: Cell division control protein 48
Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP. Determined by electron microscopy at 3.9 Å resolution. Released 3 Jul 2019.
- Method
- Electron microscopy
- Resolution
- 3.9 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 10
- Atoms
- 29,006
- Mol. weight
- 649.33 kDa
- Ligands
- ZN, ADP, ATP
- Released
- 3 Jul 2019
Explore 6OA9 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6OA9 contains 186 α-helices and 111 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: 32 helices, 12 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 | 1 |
| α-helix | 261-272 | 12 | |
| β-strand | 275-279 | 5 | 1 |
| α-helix | 282-285 | 4 | |
| α-helix | 289-305 | 17 | |
| β-strand | 309-313 | 5 | 1 |
| α-helix | 316-319 | 4 | |
| α-helix | 330-332 | 3 | |
| α-helix | 334-342 | 9 | |
| β-strand | 352-356 | 5 | 1 |
| α-helix | 365-367 | 3 | |
| β-strand | 375-378 | 4 | 1 |
| α-helix | 380-382 | 3 | |
| α-helix | 384-394 | 11 | |
| β-strand | 400 | 1 | 2 |
| α-helix | 408-412 | 5 | |
| α-helix | 418-435 | 18 | |
| β-strand | 457 | 1 | 2 |
| α-helix | 459-468 | 10 | |
| α-helix | 486-488 | 3 | |
| α-helix | 496-499 | 4 | |
| α-helix | 505-508 | 4 | |
| α-helix | 518-520 | 3 | |
| β-strand | 523-527 | 5 | 3 |
| α-helix | 536-538 | 3 | |
| β-strand | 549-552 | 4 | 3 |
| α-helix | 567-577 | 11 | |
| β-strand | 583-587 | 5 | 3 |
| α-helix | 593-596 | 4 | |
| α-helix | 611-620 | 10 | |
| α-helix | 623-625 | 3 | |
| β-strand | 629-632 | 4 | 3 |
| α-helix | 636-638 | 3 | |
| β-strand | 651-654 | 4 | 3 |
| α-helix | 664-668 | 5 | |
| α-helix | 697-703 | 7 | |
| α-helix | 706-708 | 3 | |
| α-helix | 756-759 | 4 | |
| α-helix | 760-764 | 5 | |
| α-helix | 771-778 | 8 | |
| α-helix | 785-787 | 3 | |
Chain B: 26 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 220-226 | 7 | |
| α-helix | 227-231 | 5 | |
| α-helix | 232-235 | 4 | |
| α-helix | 246-248 | 3 | |
| β-strand | 251-254 | 4 | 4 |
| α-helix | 261-270 | 10 | |
| β-strand | 277-279 | 3 | 4 |
| α-helix | 292-304 | 13 | |
| β-strand | 309-314 | 6 | 4 |
| α-helix | 316-318 | 3 | |
| α-helix | 323-325 | 3 | |
| α-helix | 330-343 | 14 | |
| β-strand | 351-356 | 6 | 4 |
| α-helix | 365-367 | 3 | |
| β-strand | 375-378 | 4 | 4 |
| α-helix | 384-392 | 9 | |
| β-strand | 400 | 1 | 5 |
| α-helix | 406-412 | 7 | |
| α-helix | 420-435 | 16 | |
| β-strand | 457 | 1 | 5 |
| α-helix | 459-468 | 10 | |
| α-helix | 496-499 | 4 | |
| α-helix | 505-508 | 4 | |
| α-helix | 511-516 | 6 | |
| α-helix | 518-520 | 3 | |
| β-strand | 523-527 | 5 | 6 |
| β-strand | 548-549 | 2 | 6 |
| α-helix | 567-578 | 12 | |
| β-strand | 582-586 | 5 | 6 |
| α-helix | 589-591 | 3 | |
| α-helix | 613-619 | 7 | |
| β-strand | 627-633 | 7 | 6 |
| α-helix | 636-638 | 3 | |
| α-helix | 641-644 | 4 | |
| β-strand | 652 | 1 | 6 |
| α-helix | 660-667 | 8 | |
| α-helix | 683-686 | 4 | |
| α-helix | 694-712 | 19 | |
Chain C: 27 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 213-215 | 3 | |
| α-helix | 220-226 | 7 | |
| α-helix | 228-231 | 4 | |
| α-helix | 237-239 | 3 | |
| α-helix | 245-248 | 4 | |
| β-strand | 250-254 | 5 | 7 |
| α-helix | 261-270 | 10 | |
| β-strand | 275-276 | 2 | 7 |
| β-strand | 279 | 1 | 7 |
| α-helix | 291-304 | 14 | |
| β-strand | 309-314 | 6 | 7 |
| α-helix | 331-343 | 13 | |
| β-strand | 351-357 | 7 | 7 |
| β-strand | 368 | 1 | 8 |
| β-strand | 373 | 1 | 8 |
| β-strand | 376-378 | 3 | 7 |
| α-helix | 387-394 | 8 | |
| α-helix | 407-410 | 4 | |
| α-helix | 419-432 | 14 | |
| α-helix | 459-467 | 9 | |
| α-helix | 486-488 | 3 | |
| α-helix | 493-498 | 6 | |
| α-helix | 499-501 | 3 | |
| α-helix | 511-516 | 6 | |
| β-strand | 523-527 | 5 | 9 |
| α-helix | 536-544 | 9 | |
| β-strand | 548-549 | 2 | 10 |
| α-helix | 554-557 | 4 | |
| α-helix | 563-565 | 3 | |
| α-helix | 568-578 | 11 | |
| β-strand | 582-583 | 2 | 10 |
| α-helix | 589-591 | 3 | |
| β-strand | 604 | 1 | 11 |
| α-helix | 611-617 | 7 | |
| α-helix | 623-625 | 3 | |
| β-strand | 629-630 | 2 | 9 |
| β-strand | 633 | 1 | 9 |
| β-strand | 651-654 | 4 | 9 |
| α-helix | 655-658 | 4 | |
| α-helix | 664-671 | 8 | |
| α-helix | 682-686 | 5 | |
| α-helix | 696-703 | 8 | |
Chain D: 22 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 213-215 | 3 | |
| α-helix | 220-227 | 8 | |
| α-helix | 232-235 | 4 | |
| α-helix | 239-243 | 5 | |
| α-helix | 246-248 | 3 | |
| β-strand | 250-254 | 5 | 12 |
| α-helix | 261-270 | 10 | |
| β-strand | 275-279 | 5 | 12 |
| α-helix | 281-284 | 4 | |
| α-helix | 292-305 | 14 | |
| β-strand | 309-313 | 5 | 12 |
| α-helix | 316-319 | 4 | |
| α-helix | 335-342 | 8 | |
| β-strand | 351-356 | 6 | 12 |
| β-strand | 375-378 | 4 | 12 |
| α-helix | 384-393 | 10 | |
| α-helix | 407-411 | 5 | |
| α-helix | 418-434 | 17 | |
| α-helix | 462-468 | 7 | |
| α-helix | 470-471 | 2 | |
| α-helix | 493-500 | 8 | |
| β-strand | 523-527 | 5 | 13 |
| α-helix | 538-542 | 5 | |
| β-strand | 548-551 | 4 | 13 |
| α-helix | 571-578 | 8 | |
| β-strand | 582-586 | 5 | 13 |
| α-helix | 610-617 | 8 | |
| β-strand | 628-632 | 5 | 13 |
| β-strand | 651-654 | 4 | 13 |
| α-helix | 662-670 | 9 | |
| α-helix | 683-688 | 6 | |
| α-helix | 694-716 | 23 | |
Chain E: 27 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 223-235 | 13 | |
| α-helix | 246-248 | 3 | |
| β-strand | 250-254 | 5 | 14 |
| α-helix | 261-272 | 12 | |
| β-strand | 275-276 | 2 | 14 |
| β-strand | 279 | 1 | 14 |
| α-helix | 281-284 | 4 | |
| α-helix | 289-304 | 16 | |
| β-strand | 309-314 | 6 | 14 |
| α-helix | 316-318 | 3 | |
| α-helix | 332-341 | 10 | |
| β-strand | 351-356 | 6 | 14 |
| α-helix | 365-367 | 3 | |
| β-strand | 375-378 | 4 | 14 |
| α-helix | 388-396 | 9 | |
| α-helix | 406-410 | 5 | |
| α-helix | 421-436 | 16 | |
| α-helix | 453-455 | 3 | |
| α-helix | 459-467 | 9 | |
| α-helix | 480-482 | 3 | |
| α-helix | 493-498 | 6 | |
| α-helix | 505-508 | 4 | |
| α-helix | 512-516 | 5 | |
| α-helix | 519-521 | 3 | |
| β-strand | 524-527 | 4 | 15 |
| α-helix | 539-542 | 4 | |
| β-strand | 548-553 | 6 | 15 |
| α-helix | 573-578 | 6 | |
| β-strand | 582-587 | 6 | 15 |
| α-helix | 589-591 | 3 | |
| α-helix | 602-620 | 19 | |
| β-strand | 629-632 | 4 | 15 |
| β-strand | 651-654 | 4 | 15 |
| α-helix | 658-659 | 2 | |
| α-helix | 664-668 | 5 | |
| α-helix | 682-686 | 5 | |
| α-helix | 704-707 | 4 | |
| α-helix | 710-712 | 3 | |
Chain F: 27 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 223-229 | 7 | |
| α-helix | 231-235 | 5 | |
| β-strand | 251-254 | 4 | 16 |
| α-helix | 261-272 | 12 | |
| β-strand | 275-280 | 6 | 16 |
| α-helix | 281-285 | 5 | |
| α-helix | 289-300 | 12 | |
| α-helix | 301-303 | 3 | |
| β-strand | 309-314 | 6 | 16 |
| α-helix | 333-342 | 10 | |
| β-strand | 352-357 | 6 | 16 |
| α-helix | 360-362 | 3 | |
| β-strand | 376-378 | 3 | 16 |
| α-helix | 386-394 | 9 | |
| β-strand | 400 | 1 | 17 |
| α-helix | 408-412 | 5 | |
| α-helix | 418-434 | 17 | |
| β-strand | 457 | 1 | 17 |
| α-helix | 459-466 | 8 | |
| α-helix | 486-488 | 3 | |
| α-helix | 493-500 | 8 | |
| α-helix | 511-514 | 4 | |
| β-strand | 523-527 | 5 | 18 |
| α-helix | 534-539 | 6 | |
| α-helix | 541-544 | 4 | |
| β-strand | 550-551 | 2 | 18 |
| α-helix | 556-559 | 4 | |
| α-helix | 568-571 | 4 | |
| α-helix | 573-578 | 6 | |
| β-strand | 582-585 | 4 | 18 |
| α-helix | 611-617 | 7 | |
| β-strand | 627-630 | 4 | 18 |
| β-strand | 649-654 | 6 | 18 |
| α-helix | 657-659 | 3 | |
| α-helix | 660-670 | 11 | |
| α-helix | 683-686 | 4 | |
| α-helix | 700-703 | 4 | |
| α-helix | 704-706 | 3 | |
| α-helix | 710-713 | 4 | |
Chain G: 19 helices, 24 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 117-124 | 8 | |
| β-strand | 129 | 1 | 23 |
| β-strand | 143-144 | 2 | 12 |
| α-helix | 150 | 1 | |
| β-strand | 151 | 1 | 23 |
| α-helix | 152 | 1 | |
| α-helix | 156-161 | 6 | |
| α-helix | 169-180 | 12 | |
| α-helix | 195-197 | 3 | |
| α-helix | 221-223 | 3 | |
| β-strand | 224 | 1 | 24 |
| α-helix | 227-229 | 3 | |
| β-strand | 236-238 | 3 | 25 |
| α-helix | 244-255 | 12 | |
| β-strand | 260-270 | 11 | 25 |
| β-strand | 276-285 | 10 | 25 |
| β-strand | 291 | 1 | 26 |
| β-strand | 296 | 1 | 26 |
| α-helix | 300-317 | 18 | |
| β-strand | 320-327 | 8 | 25 |
| α-helix | 352-364 | 13 | |
| β-strand | 368 | 1 | 27 |
| β-strand | 376 | 1 | 27 |
| β-strand | 382-386 | 5 | 25 |
| β-strand | 397-398 | 2 | 25 |
| β-strand | 399-401 | 3 | 28 |
| α-helix | 406-409 | 4 | |
| β-strand | 415 | 1 | 29 |
| β-strand | 422-423 | 2 | 30 |
| β-strand | 424 | 1 | 29 |
| β-strand | 437 | 1 | 24 |
| β-strand | 442 | 1 | 31 |
| β-strand | 447 | 1 | 31 |
| β-strand | 457-458 | 2 | 30 |
| β-strand | 463-465 | 3 | 28 |
| β-strand | 469 | 1 | 25 |
| α-helix | 488-489 | 2 | |
| α-helix | 502-507 | 6 | |
| α-helix | 517-524 | 8 | |
| α-helix | 527-536 | 10 | |
| α-helix | 541-552 | 12 | |
| α-helix | 557-565 | 9 | |
| α-helix | 567-578 | 12 | |
Chain H: 2 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 102-106 | 5 | 19 |
| β-strand | 112-116 | 5 | 19 |
| β-strand | 122 | 1 | 20 |
| α-helix | 123-134 | 12 | |
| β-strand | 141-145 | 5 | 19 |
| β-strand | 148-149 | 2 | 19 |
| α-helix | 150-151 | 2 | |
| β-strand | 155 | 1 | 20 |
| β-strand | 166-171 | 6 | 19 |
2 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) |
| Ubiquitin | H, J, K | protein | 76 | Saccharomyces cerevisiae | P0CH08 (AlphaFold model) |
| Nuclear protein localization protein 4 | G | protein | 580 | Saccharomyces cerevisiae | P33755 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F), FASTA
>6OA9_1 Cell division control protein 48 (chains A, B, C, D, E, F)
MGEEHKPLLDASGVDPREEDKTATAILRRKKKDNMLLVDDAINDDNSVIAINSNTMDKLE
LFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKY
ATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEP
EEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLF
KAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAF
EEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRP
NSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGAD
IASLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVE
SVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKA
VATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDQLDSIAKARGGSL
GDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDE
NARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHE
AEKEVKVEGEDVEMTDEGAKAEQEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAY
SQQMKASRGQFSNFNFNDAPLGTTATDNANSNNSAPSGAGAAFGSNAEEDDDLYS
Sequence of entity 2 (H, J, K), FASTA
>6OA9_2 Ubiquitin (chains H, J, K)
MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
Sequence of entity 3 (G), FASTA
>6OA9_3 Nuclear protein localization protein 4 (chains G)
MLIRFRSKNGTHRVSCQENDLFGTVIEKLVGNLDPNADVDTFTVCEKPGQGIHAVSELAD
RTVMDLGLKHGDMLILNYSDKPANEKDGVNVEIGSVGIDSKGIRQHRYGPLRIKELAVDE
ELEKEDGLIPRQKSKLCKHGDRGMCEYCSPLPPWDKEYHEKNKIKHISFHSYLKKLNENA
NKKENGSSYISPLSEPDFRINKRCHNGHEPWPRGICSKCQPSAITLQQQEFRMVDHVEFQ
KSEIINEFIQAWRYTGMQRFGYMYGSYSKYDNTPLGIKAVVEAIYEPPQHDEQDGLTMDV
EQVKNEMLQIDRQAQEMGLSRIGLIFTDLSDAGAGDGSVFCKRHKDSFFLSSLEVIMAAR
HQTRHPNVSKYSEQGFFSSKFVTCVISGNLEGEIDISSYQVSTEAEALVTADMISGSTFP
SMAYINDTTDERYVPEIFYMKSNEYGITVKENAKPAFPVDYLLVTLTHGFPNTDTETNSK
FVSSTGFPWSNRQAMGQSQDYQELKKYLFNVASSGDFNLLHEKISNFHLLLYINSLQILS
PDEWKLLIESAVKNEWEESLLKLVSSAGWQTLVMILQESG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 1 |
| ATP | Adenosine-5'-triphosphate | C10 H16 N5 O13 P3 | 9 |
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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