8U7T: Substrate-bound Cdc48, Class 1
Substrate-bound Cdc48, Class 1. Determined by electron microscopy at 3.3 Å resolution. Released 6 Nov 2024.
- Method
- Electron microscopy
- Resolution
- 3.3 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 7
- Atoms
- 22,540
- Mol. weight
- 559.39 kDa
- Ligands
- ADP, MG, 08T
- Released
- 6 Nov 2024
Explore 8U7T in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8U7T contains 173 α-helices and 86 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, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 462-464 | 3 | |
| α-helix | 469-484 | 16 | |
| α-helix | 487-492 | 6 | |
| α-helix | 495-497 | 3 | |
| β-strand | 500-503 | 4 | 4 |
| α-helix | 510-520 | 11 | |
| β-strand | 525-529 | 5 | 4 |
| α-helix | 530-532 | 3 | |
| α-helix | 540-555 | 16 | |
| β-strand | 559-563 | 5 | 4 |
| α-helix | 565-568 | 4 | |
| α-helix | 579-592 | 14 | |
| α-helix | 596-598 | 3 | |
| β-strand | 601-605 | 5 | 4 |
| α-helix | 614-617 | 4 | |
| β-strand | 624-627 | 4 | 4 |
| α-helix | 633-643 | 11 | |
| α-helix | 669-685 | 17 | |
| α-helix | 709-717 | 9 | |
| α-helix | 724-726 | 3 | |
| α-helix | 742-757 | 16 | |
| α-helix | 759-765 | 7 | |
| α-helix | 768-770 | 3 | |
| β-strand | 772-776 | 5 | 5 |
| α-helix | 783-793 | 11 | |
| β-strand | 799-802 | 4 | 5 |
| α-helix | 803-805 | 3 | |
| α-helix | 813-827 | 15 | |
| β-strand | 831-836 | 6 | 5 |
| α-helix | 852-854 | 3 | |
| α-helix | 855-867 | 13 | |
| β-strand | 876-882 | 7 | 5 |
| α-helix | 885-887 | 3 | |
| α-helix | 890-893 | 4 | |
| β-strand | 901-903 | 3 | 5 |
| α-helix | 909-919 | 11 | |
| β-strand | 925 | 1 | 6 |
| α-helix | 932-937 | 6 | |
| α-helix | 943-973 | 31 | |
| β-strand | 1002 | 1 | 6 |
| α-helix | 1004-1010 | 7 | |
| α-helix | 1011-1013 | 3 | |
| α-helix | 1020-1031 | 12 | |
Chain B: 29 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 999-1013 | 15 | |
| α-helix | 1015-1021 | 7 | |
| β-strand | 1028-1032 | 5 | 7 |
| α-helix | 1039-1049 | 11 | |
| β-strand | 1053-1057 | 5 | 7 |
| α-helix | 1060-1062 | 3 | |
| β-strand | 1066 | 1 | 8 |
| α-helix | 1069-1084 | 16 | |
| β-strand | 1087-1091 | 5 | 7 |
| α-helix | 1094-1096 | 3 | |
| α-helix | 1108-1120 | 13 | |
| β-strand | 1129-1134 | 6 | 7 |
| α-helix | 1138-1140 | 3 | |
| α-helix | 1143-1145 | 3 | |
| β-strand | 1153-1156 | 4 | 7 |
| α-helix | 1162-1172 | 11 | |
| β-strand | 1178 | 1 | 9 |
| α-helix | 1184-1190 | 7 | |
| α-helix | 1197-1213 | 17 | |
| α-helix | 1220-1223 | 4 | |
| β-strand | 1228 | 1 | 9 |
| α-helix | 1230-1239 | 10 | |
| α-helix | 1243-1246 | 4 | |
| α-helix | 1249-1252 | 4 | |
| α-helix | 1264-1279 | 16 | |
| α-helix | 1281-1287 | 7 | |
| α-helix | 1290-1292 | 3 | |
| β-strand | 1295-1298 | 4 | 10 |
| α-helix | 1305-1314 | 10 | |
| β-strand | 1319-1323 | 5 | 10 |
| β-strand | 1332 | 1 | 11 |
| α-helix | 1335-1349 | 15 | |
| β-strand | 1353-1358 | 6 | 10 |
| α-helix | 1360-1362 | 3 | |
| α-helix | 1377-1389 | 13 | |
| β-strand | 1398-1403 | 6 | 10 |
| α-helix | 1412-1415 | 4 | |
| β-strand | 1422-1425 | 4 | 10 |
| α-helix | 1431-1441 | 11 | |
| β-strand | 1447 | 1 | 12 |
| α-helix | 1454-1459 | 6 | |
| α-helix | 1465-1492 | 28 | |
| β-strand | 1499 | 1 | 12 |
| α-helix | 1501-1507 | 7 | |
| α-helix | 1517-1533 | 17 | |
Chain C: 33 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1546-1548 | 3 | |
| α-helix | 1553-1568 | 16 | |
| α-helix | 1571-1576 | 6 | |
| α-helix | 1579-1581 | 3 | |
| β-strand | 1583-1587 | 5 | 13 |
| α-helix | 1594-1604 | 11 | |
| β-strand | 1608-1613 | 6 | 13 |
| α-helix | 1615-1617 | 3 | |
| α-helix | 1625-1639 | 15 | |
| β-strand | 1642-1647 | 6 | 13 |
| α-helix | 1649-1651 | 3 | |
| α-helix | 1662-1675 | 14 | |
| β-strand | 1685-1690 | 6 | 13 |
| α-helix | 1698-1700 | 3 | |
| β-strand | 1708-1711 | 4 | 13 |
| α-helix | 1717-1727 | 11 | |
| α-helix | 1740-1745 | 6 | |
| α-helix | 1752-1772 | 21 | |
| α-helix | 1782-1785 | 4 | |
| α-helix | 1792-1801 | 10 | |
| α-helix | 1805-1807 | 3 | |
| α-helix | 1811-1813 | 3 | |
| α-helix | 1826-1841 | 16 | |
| α-helix | 1843-1849 | 7 | |
| α-helix | 1852-1854 | 3 | |
| β-strand | 1857-1860 | 4 | 14 |
| α-helix | 1867-1877 | 11 | |
| β-strand | 1881-1885 | 5 | 14 |
| β-strand | 1894 | 1 | 15 |
| α-helix | 1897-1911 | 15 | |
| β-strand | 1915-1920 | 6 | 14 |
| α-helix | 1922-1925 | 4 | |
| β-strand | 1927 | 1 | 16 |
| α-helix | 1928 | 1 | |
| α-helix | 1939-1951 | 13 | |
| β-strand | 1960-1966 | 7 | 14 |
| α-helix | 1969-1971 | 3 | |
| β-strand | 1972 | 1 | 16 |
| α-helix | 1974-1977 | 4 | |
| β-strand | 1984-1987 | 4 | 14 |
| α-helix | 1993-2003 | 11 | |
| β-strand | 2009 | 1 | 17 |
| α-helix | 2016-2022 | 7 | |
| α-helix | 2027-2052 | 26 | |
| β-strand | 2061 | 1 | 17 |
| α-helix | 2063-2069 | 7 | |
| α-helix | 2070-2072 | 3 | |
| α-helix | 2079-2094 | 16 | |
Chain D: 30 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2111-2126 | 16 | |
| α-helix | 2129-2134 | 6 | |
| α-helix | 2137-2139 | 3 | |
| β-strand | 2142-2144 | 3 | 18 |
| β-strand | 2145 | 1 | 19 |
| α-helix | 2152-2162 | 11 | |
| β-strand | 2166-2171 | 6 | 18 |
| α-helix | 2183-2197 | 15 | |
| β-strand | 2200-2205 | 6 | 18 |
| α-helix | 2207-2209 | 3 | |
| α-helix | 2220-2233 | 14 | |
| β-strand | 2242-2247 | 6 | 18 |
| α-helix | 2256-2258 | 3 | |
| β-strand | 2266 | 1 | 18 |
| β-strand | 2269 | 1 | 19 |
| α-helix | 2275-2285 | 11 | |
| α-helix | 2297-2303 | 7 | |
| α-helix | 2310-2327 | 18 | |
| α-helix | 2340-2343 | 4 | |
| α-helix | 2350-2359 | 10 | |
| α-helix | 2364-2366 | 3 | |
| α-helix | 2369-2371 | 3 | |
| α-helix | 2377-2379 | 3 | |
| α-helix | 2384-2399 | 16 | |
| α-helix | 2401-2407 | 7 | |
| α-helix | 2410-2412 | 3 | |
| β-strand | 2415-2418 | 4 | 20 |
| α-helix | 2425-2434 | 10 | |
| β-strand | 2439-2443 | 5 | 20 |
| α-helix | 2446-2448 | 3 | |
| β-strand | 2452 | 1 | 21 |
| α-helix | 2456-2469 | 14 | |
| β-strand | 2473-2478 | 6 | 20 |
| α-helix | 2480-2483 | 4 | |
| α-helix | 2493-2509 | 17 | |
| β-strand | 2518-2524 | 7 | 20 |
| α-helix | 2527-2529 | 3 | |
| β-strand | 2542-2545 | 4 | 20 |
| α-helix | 2551-2561 | 11 | |
| β-strand | 2567 | 1 | 22 |
| α-helix | 2573-2578 | 6 | |
| α-helix | 2585-2606 | 22 | |
| β-strand | 2644 | 1 | 22 |
| α-helix | 2646-2654 | 9 | |
| α-helix | 2662-2673 | 12 | |
Chain E: 26 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2675-2677 | 3 | |
| α-helix | 2682-2697 | 16 | |
| α-helix | 2700-2705 | 6 | |
| α-helix | 2708-2710 | 3 | |
| β-strand | 2713-2716 | 4 | 24 |
| α-helix | 2723-2733 | 11 | |
| β-strand | 2738-2741 | 4 | 24 |
| α-helix | 2743-2746 | 4 | |
| α-helix | 2754-2768 | 15 | |
| β-strand | 2772-2776 | 5 | 24 |
| α-helix | 2778-2781 | 4 | |
| α-helix | 2791-2804 | 14 | |
| β-strand | 2814-2819 | 6 | 24 |
| β-strand | 2837-2840 | 4 | 24 |
| α-helix | 2846-2856 | 11 | |
| α-helix | 2868-2874 | 7 | |
| α-helix | 2881-2897 | 17 | |
| α-helix | 2921-2929 | 9 | |
| α-helix | 2955-2970 | 16 | |
| α-helix | 2972-2978 | 7 | |
| α-helix | 2981-2983 | 3 | |
| β-strand | 2986-2989 | 4 | 25 |
| α-helix | 2996-3005 | 10 | |
| β-strand | 3010-3014 | 5 | 25 |
| β-strand | 3023 | 1 | 23 |
| α-helix | 3026-3040 | 15 | |
| β-strand | 3044-3049 | 6 | 25 |
| α-helix | 3051-3054 | 4 | |
| α-helix | 3064-3080 | 17 | |
| β-strand | 3090-3095 | 6 | 25 |
| α-helix | 3098-3100 | 3 | |
| β-strand | 3113-3116 | 4 | 25 |
| α-helix | 3122-3132 | 11 | |
| α-helix | 3144-3149 | 6 | |
| α-helix | 3156-3174 | 19 | |
| α-helix | 3217-3225 | 9 | |
| α-helix | 3234-3248 | 15 | |
Chain F: 24 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-15 | 14 | |
| α-helix | 17-23 | 7 | |
| β-strand | 30-34 | 5 | 1 |
| α-helix | 41-51 | 11 | |
| β-strand | 56-60 | 5 | 1 |
| α-helix | 62-64 | 3 | |
| α-helix | 69-83 | 15 | |
| β-strand | 87-91 | 5 | 1 |
| α-helix | 93-96 | 4 | |
| α-helix | 103-115 | 13 | |
| β-strand | 124-128 | 5 | 1 |
| β-strand | 147-150 | 4 | 1 |
| α-helix | 154-164 | 11 | |
| α-helix | 165-167 | 3 | |
| α-helix | 176-182 | 7 | |
| α-helix | 190-205 | 16 | |
| α-helix | 211-219 | 9 | |
| α-helix | 224-238 | 15 | |
| α-helix | 242-246 | 5 | |
| β-strand | 250-253 | 4 | 2 |
| α-helix | 258-267 | 10 | |
| β-strand | 274-276 | 3 | 2 |
| α-helix | 279-281 | 3 | |
| α-helix | 284-298 | 15 | |
| β-strand | 302-307 | 6 | 2 |
| α-helix | 309-313 | 5 | |
| α-helix | 322-338 | 17 | |
| β-strand | 347-353 | 7 | 2 |
| β-strand | 373-374 | 2 | 2 |
| α-helix | 377-387 | 11 | |
| β-strand | 393 | 1 | 3 |
| α-helix | 400-405 | 6 | |
| α-helix | 411-436 | 26 | |
| β-strand | 447 | 1 | 3 |
| α-helix | 449-455 | 7 | |
| α-helix | 456-458 | 3 | |
Chain G: 0 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2652 | 1 | 8 |
| β-strand | 2664 | 1 | 11 |
| β-strand | 2666 | 1 | 15 |
| β-strand | 2668 | 1 | 21 |
| β-strand | 2670 | 1 | 23 |
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 | 23 | Saccharomyces cerevisiae | |
Sequence of entity 1 (A, B, C, D, E, F), FASTA
>8U7T_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
>8U7T_2 Substrate (chains G)
AAAAAAAAAAAAAVAVAVAVAAA
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:
- 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
- 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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