9W8R: Yeast Pol II
Structure of yeast Pol II in complex with a short control scaffold lacking cisplatin-ICL lesion. Determined by electron microscopy at 2.68 Å resolution. Released 24 Jun 2026.
- Method
- Electron microscopy
- Resolution
- 2.68 Å
- Organisms
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c), synthetic construct
- Chains
- 15
- Atoms
- 32,477
- Mol. weight
- 528.63 kDa
- Ligands
- MG, ZN
- Released
- 24 Jun 2026
Explore 9W8R in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9W8R contains 195 α-helices and 232 β-strands across 12 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: 80 helices, 71 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10 | 1 | |
| β-strand | 11 | 1 | 22 |
| β-strand | 16-18 | 3 | 23 |
| α-helix | 24-30 | 7 | |
| β-strand | 34 | 1 | 24 |
| β-strand | 41 | 1 | 25 |
| β-strand | 48 | 1 | 25 |
| α-helix | 49 | 1 | |
| α-helix | 56-58 | 3 | |
| β-strand | 82-91 | 10 | 24 |
| α-helix | 93-95 | 3 | |
| α-helix | 96-105 | 10 | |
| β-strand | 106 | 1 | 26 |
| β-strand | 113 | 1 | 26 |
| α-helix | 120-126 | 7 | |
| α-helix | 131-142 | 12 | |
| β-strand | 151-153 | 3 | 27 |
| β-strand | 161-163 | 3 | 27 |
| α-helix | 169-172 | 4 | |
| β-strand | 173-177 | 5 | 28 |
| β-strand | 180-185 | 6 | 28 |
| α-helix | 186-187 | 2 | |
| β-strand | 198-201 | 4 | 28 |
| α-helix | 204-212 | 9 | |
| α-helix | 216-221 | 6 | |
| β-strand | 225 | 1 | 29 |
| β-strand | 229 | 1 | 29 |
| α-helix | 231-234 | 4 | |
| β-strand | 235-241 | 7 | 24 |
| α-helix | 261-282 | 22 | |
| α-helix | 286-304 | 19 | |
| α-helix | 312-313 | 2 | |
| β-strand | 315 | 1 | 30 |
| β-strand | 321 | 1 | 30 |
| α-helix | 325-329 | 5 | |
| α-helix | 335 | 1 | |
| α-helix | 336-341 | 6 | |
| β-strand | 343-345 | 3 | 31 |
| β-strand | 348-355 | 8 | 32 |
| β-strand | 363-367 | 5 | 32 |
| α-helix | 368-373 | 6 | |
| β-strand | 375-379 | 5 | 33 |
| α-helix | 380 | 1 | |
| α-helix | 385-394 | 10 | |
| β-strand | 402-406 | 5 | 33 |
| β-strand | 412-414 | 3 | 33 |
| β-strand | 431-435 | 5 | 33 |
| α-helix | 436 | 1 | |
| β-strand | 441-445 | 5 | 32 |
| α-helix | 452-454 | 3 | |
| β-strand | 455-463 | 9 | 32 |
| β-strand | 468-470 | 3 | 32 |
| α-helix | 475-478 | 4 | |
| β-strand | 486-490 | 5 | 32 |
| α-helix | 495-504 | 10 | |
| β-strand | 506 | 1 | 32 |
| α-helix | 508-510 | 3 | |
| β-strand | 512-513 | 2 | 34 |
| β-strand | 518-519 | 2 | 34 |
| α-helix | 526-534 | 9 | |
| β-strand | 540-541 | 2 | 35 |
| α-helix | 543-551 | 9 | |
| α-helix | 560-563 | 4 | |
| β-strand | 565-567 | 3 | 36 |
| β-strand | 571 | 1 | 36 |
| β-strand | 572-573 | 2 | 35 |
| α-helix | 574-581 | 8 | |
| α-helix | 583 | 1 | |
| β-strand | 588-590 | 3 | 37 |
| β-strand | 605-608 | 4 | 37 |
| β-strand | 611-614 | 4 | 37 |
| α-helix | 619-622 | 4 | |
| α-helix | 629-636 | 8 | |
| α-helix | 639-660 | 22 | |
| β-strand | 663 | 1 | 38 |
| α-helix | 666-669 | 4 | |
| α-helix | 673-698 | 26 | |
| α-helix | 702-705 | 4 | |
| α-helix | 710-736 | 27 | |
| α-helix | 742-749 | 8 | |
| α-helix | 755-758 | 4 | |
| α-helix | 759-763 | 5 | |
| β-strand | 766-767 | 2 | 39 |
| β-strand | 769-770 | 2 | 40 |
| β-strand | 773-774 | 2 | 40 |
| α-helix | 775-776 | 2 | |
| β-strand | 779 | 1 | 41 |
| β-strand | 782 | 1 | 41 |
| β-strand | 799-800 | 2 | 39 |
| α-helix | 810-845 | 36 | |
| β-strand | 849-850 | 2 | 42 |
| β-strand | 856-857 | 2 | 42 |
| β-strand | 863-865 | 3 | 42 |
| α-helix | 868-870 | 3 | |
| β-strand | 873 | 1 | 43 |
| α-helix | 875-877 | 3 | |
| β-strand | 879-882 | 4 | 44 |
| α-helix | 890-897 | 8 | |
| β-strand | 913 | 1 | 45 |
| α-helix | 916-919 | 4 | |
| α-helix | 924-946 | 23 | |
| β-strand | 953-956 | 4 | 44 |
| α-helix | 960-971 | 12 | |
| α-helix | 978 | 1 | |
| β-strand | 979 | 1 | 45 |
| α-helix | 983-994 | 12 | |
| α-helix | 1005-1014 | 10 | |
| α-helix | 1016-1025 | 10 | |
| α-helix | 1028-1029 | 2 | |
| α-helix | 1030-1035 | 6 | |
| α-helix | 1039-1055 | 17 | |
| β-strand | 1057 | 1 | 43 |
| α-helix | 1058-1059 | 2 | |
| α-helix | 1064-1078 | 15 | |
| α-helix | 1097-1105 | 9 | |
| β-strand | 1115-1119 | 5 | 46 |
| β-strand | 1120 | 1 | 47 |
| α-helix | 1122-1124 | 3 | |
| α-helix | 1128-1138 | 11 | |
| β-strand | 1141 | 1 | 48 |
| α-helix | 1143-1145 | 3 | |
| β-strand | 1147-1154 | 8 | 16 |
| α-helix | 1167-1176 | 10 | |
| α-helix | 1185-1187 | 3 | |
| β-strand | 1188 | 1 | 49 |
| β-strand | 1191-1197 | 7 | 16 |
| α-helix | 1201-1204 | 4 | |
| α-helix | 1209-1220 | 12 | |
| β-strand | 1224-1228 | 5 | 16 |
| β-strand | 1237-1242 | 6 | 16 |
| β-strand | 1243 | 1 | 49 |
| α-helix | 1244-1245 | 2 | |
| α-helix | 1256-1268 | 13 | |
| β-strand | 1274 | 1 | 48 |
| β-strand | 1281-1292 | 12 | 46 |
| α-helix | 1293 | 1 | |
| β-strand | 1298-1309 | 12 | 46 |
| α-helix | 1313-1317 | 5 | |
| β-strand | 1322 | 1 | 47 |
| β-strand | 1328-1329 | 2 | 46 |
| α-helix | 1332-1339 | 8 | |
| α-helix | 1341-1358 | 18 | |
| α-helix | 1365-1375 | 11 | |
| α-helix | 1389-1391 | 3 | |
| α-helix | 1396-1400 | 5 | |
| α-helix | 1405-1415 | 11 | |
| β-strand | 1418-1419 | 2 | 23 |
| α-helix | 1424-1430 | 7 | |
| α-helix | 1437-1439 | 3 | |
| β-strand | 1441-1445 | 5 | 10 |
| α-helix | 1447-1453 | 7 | |
Chain B: 56 helices, 82 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 23 | 1 | |
| β-strand | 24 | 1 | 50 |
| α-helix | 25-26 | 2 | |
| α-helix | 30-40 | 11 | |
| α-helix | 45-53 | 9 | |
| α-helix | 54-58 | 5 | |
| α-helix | 59-64 | 6 | |
| β-strand | 68-73 | 6 | 51 |
| α-helix | 80-82 | 3 | |
| β-strand | 84-97 | 14 | 51 |
| β-strand | 101-102 | 2 | 52 |
| β-strand | 110-111 | 2 | 52 |
| α-helix | 114-120 | 7 | |
| β-strand | 125-140 | 16 | 51 |
| α-helix | 146-147 | 2 | |
| β-strand | 150-151 | 2 | 51 |
| β-strand | 156 | 1 | 51 |
| β-strand | 164-171 | 8 | 51 |
| α-helix | 186-191 | 6 | |
| β-strand | 203-205 | 3 | 53 |
| β-strand | 208-212 | 5 | 53 |
| α-helix | 213 | 1 | |
| β-strand | 214-218 | 5 | 54 |
| α-helix | 219 | 1 | |
| β-strand | 223-227 | 5 | 55 |
| β-strand | 234-242 | 9 | 55 |
| β-strand | 252-259 | 8 | 55 |
| β-strand | 269-272 | 4 | 55 |
| β-strand | 276 | 1 | 56 |
| β-strand | 280-281 | 2 | 55 |
| α-helix | 282-289 | 8 | |
| α-helix | 294-301 | 8 | |
| α-helix | 308-321 | 14 | |
| α-helix | 327-336 | 10 | |
| β-strand | 338 | 1 | 56 |
| α-helix | 348-358 | 11 | |
| α-helix | 371-389 | 19 | |
| α-helix | 394-397 | 4 | |
| α-helix | 401-403 | 3 | |
| β-strand | 404-407 | 4 | 54 |
| α-helix | 409-437 | 29 | |
| α-helix | 444-447 | 4 | |
| α-helix | 450-462 | 13 | |
| β-strand | 480-482 | 3 | 53 |
| α-helix | 483-484 | 2 | |
| α-helix | 488-494 | 7 | |
| β-strand | 497-499 | 3 | 54 |
| α-helix | 516-518 | 3 | |
| β-strand | 522 | 1 | 57 |
| β-strand | 533 | 1 | 54 |
| β-strand | 536-538 | 3 | 54 |
| β-strand | 539 | 1 | 57 |
| β-strand | 544-545 | 2 | 58 |
| α-helix | 552-560 | 9 | |
| α-helix | 563 | 1 | |
| β-strand | 564-565 | 2 | 59 |
| β-strand | 578-582 | 5 | 59 |
| β-strand | 585-590 | 6 | 59 |
| α-helix | 593-605 | 13 | |
| β-strand | 614-618 | 5 | 59 |
| β-strand | 623-627 | 5 | 59 |
| β-strand | 633-639 | 7 | 58 |
| β-strand | 640-641 | 2 | 60 |
| β-strand | 650-651 | 2 | 60 |
| β-strand | 654 | 1 | 50 |
| α-helix | 655-668 | 14 | |
| α-helix | 681-686 | 6 | |
| β-strand | 690-694 | 5 | 58 |
| α-helix | 697-700 | 4 | |
| β-strand | 703-704 | 2 | 58 |
| α-helix | 707-710 | 4 | |
| α-helix | 728-729 | 2 | |
| β-strand | 740-741 | 2 | 58 |
| α-helix | 745-748 | 4 | |
| α-helix | 759-761 | 3 | |
| α-helix | 764-773 | 10 | |
| β-strand | 777 | 1 | 61 |
| α-helix | 785-787 | 3 | |
| β-strand | 792-796 | 5 | 21 |
| β-strand | 800 | 1 | 19 |
| β-strand | 804-805 | 2 | 62 |
| α-helix | 807-809 | 3 | |
| β-strand | 821-827 | 7 | 63 |
| β-strand | 828 | 1 | 38 |
| β-strand | 838-842 | 5 | 63 |
| α-helix | 843-847 | 5 | |
| β-strand | 853-862 | 10 | 21 |
| β-strand | 865 | 1 | 64 |
| β-strand | 871 | 1 | 64 |
| β-strand | 873-874 | 2 | 65 |
| β-strand | 883 | 1 | 65 |
| β-strand | 898 | 1 | 66 |
| α-helix | 899-900 | 2 | |
| β-strand | 904-905 | 2 | 21 |
| β-strand | 910-912 | 3 | 66 |
| β-strand | 914-917 | 4 | 65 |
| β-strand | 924 | 1 | 67 |
| β-strand | 928 | 1 | 67 |
| β-strand | 934-936 | 3 | 65 |
| β-strand | 939-940 | 2 | 66 |
| α-helix | 941-942 | 2 | |
| β-strand | 947-956 | 10 | 21 |
| β-strand | 962-972 | 11 | 21 |
| β-strand | 979-982 | 4 | 63 |
| β-strand | 987-994 | 8 | 63 |
| α-helix | 996-998 | 3 | |
| β-strand | 1001-1002 | 2 | 68 |
| β-strand | 1010-1012 | 3 | 63 |
| α-helix | 1016-1020 | 5 | |
| α-helix | 1023-1038 | 16 | |
| β-strand | 1042-1043 | 2 | 62 |
| α-helix | 1052-1061 | 10 | |
| β-strand | 1069-1070 | 2 | 63 |
| β-strand | 1072-1073 | 2 | 68 |
| α-helix | 1079 | 1 | |
| β-strand | 1080 | 1 | 68 |
| α-helix | 1081 | 1 | |
| α-helix | 1084 | 1 | |
| β-strand | 1085-1094 | 10 | 63 |
| β-strand | 1095 | 1 | 61 |
| α-helix | 1099-1101 | 3 | |
| β-strand | 1104-1106 | 3 | 32 |
| β-strand | 1111 | 1 | 69 |
| β-strand | 1118 | 1 | 69 |
| α-helix | 1119 | 1 | |
| α-helix | 1122-1124 | 3 | |
| β-strand | 1128-1130 | 3 | 31 |
| α-helix | 1132-1141 | 10 | |
| α-helix | 1144-1148 | 5 | |
| α-helix | 1149-1153 | 5 | |
| β-strand | 1158-1163 | 6 | 22 |
| β-strand | 1172-1174 | 3 | 70 |
| β-strand | 1179-1181 | 3 | 70 |
| β-strand | 1182 | 1 | 71 |
| β-strand | 1187 | 1 | 71 |
| β-strand | 1191-1196 | 6 | 22 |
| α-helix | 1198-1209 | 12 | |
| β-strand | 1215-1217 | 3 | 23 |
Chain C: 13 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-13 | 7 | 1 |
| β-strand | 17-23 | 7 | 1 |
| α-helix | 27-39 | 13 | |
| β-strand | 43-54 | 12 | 2 |
| α-helix | 60-68 | 9 | |
| β-strand | 72-74 | 3 | 3 |
| α-helix | 77-79 | 3 | |
| β-strand | 97-104 | 8 | 2 |
| α-helix | 110 | 1 | |
| β-strand | 111-113 | 3 | 4 |
| α-helix | 115-117 | 3 | |
| β-strand | 119-120 | 2 | 2 |
| β-strand | 129-132 | 4 | 3 |
| α-helix | 133 | 1 | |
| β-strand | 145-147 | 3 | 4 |
| β-strand | 152-162 | 11 | 2 |
| α-helix | 168-170 | 3 | |
| β-strand | 176-179 | 4 | 1 |
| α-helix | 197-200 | 4 | |
| α-helix | 202-204 | 3 | |
| α-helix | 205-209 | 5 | |
| α-helix | 211-213 | 3 | |
| α-helix | 218-219 | 2 | |
| β-strand | 228-233 | 6 | 1 |
| α-helix | 240-266 | 27 | |
Chain D: 9 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 20-22 | 3 | |
| β-strand | 23 | 1 | 72 |
| β-strand | 28 | 1 | 72 |
| β-strand | 36-38 | 3 | 73 |
| β-strand | 44-46 | 3 | 73 |
| β-strand | 49 | 1 | 10 |
| α-helix | 52-72 | 21 | |
| α-helix | 119-133 | 15 | |
| α-helix | 139-150 | 12 | |
| α-helix | 157-170 | 14 | |
| α-helix | 174-182 | 9 | |
| α-helix | 188-194 | 7 | |
| α-helix | 196-198 | 3 | |
| α-helix | 204-216 | 13 | |
Chain E: 12 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-25 | 23 | |
| β-strand | 28 | 1 | 5 |
| α-helix | 32-35 | 4 | |
| α-helix | 39-46 | 8 | |
| β-strand | 47 | 1 | 6 |
| β-strand | 53 | 1 | 6 |
| β-strand | 60-62 | 3 | 7 |
| β-strand | 64 | 1 | 5 |
| α-helix | 66-71 | 6 | |
| β-strand | 78-82 | 5 | 7 |
| β-strand | 87-88 | 2 | 8 |
| α-helix | 90-102 | 13 | |
| β-strand | 107-112 | 6 | 7 |
| β-strand | 115-116 | 2 | 8 |
| α-helix | 118-121 | 4 | |
| β-strand | 131-136 | 6 | 7 |
| α-helix | 138-140 | 3 | |
| α-helix | 144-146 | 3 | |
| β-strand | 152-155 | 4 | 9 |
| α-helix | 156-157 | 2 | |
| α-helix | 158-167 | 10 | |
| α-helix | 176 | 1 | |
| β-strand | 177-178 | 2 | 9 |
| α-helix | 183-188 | 6 | |
| β-strand | 195-200 | 6 | 9 |
| β-strand | 208-214 | 7 | 9 |
Chain F: 5 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 73 | 1 | 10 |
| α-helix | 76-78 | 3 | |
| β-strand | 84 | 1 | 11 |
| α-helix | 85-86 | 2 | |
| α-helix | 87-102 | 16 | |
| α-helix | 105-107 | 3 | |
| α-helix | 117-126 | 10 | |
| β-strand | 132-137 | 6 | 10 |
| β-strand | 143-147 | 5 | 10 |
| β-strand | 152 | 1 | 11 |
Chain G: 4 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-13 | 12 | 10 |
| α-helix | 15-17 | 3 | |
| α-helix | 22-30 | 9 | |
| β-strand | 37-39 | 3 | 10 |
| β-strand | 43-49 | 7 | 10 |
| β-strand | 55 | 1 | 10 |
| β-strand | 60-61 | 2 | 10 |
| α-helix | 62 | 1 | |
| β-strand | 68-79 | 12 | 10 |
| β-strand | 85-94 | 10 | 12 |
| β-strand | 98-103 | 6 | 12 |
| β-strand | 106-111 | 6 | 12 |
| α-helix | 112-114 | 3 | |
| β-strand | 120-122 | 3 | 13 |
| β-strand | 129-131 | 3 | 13 |
| β-strand | 136 | 1 | 13 |
| β-strand | 142-152 | 11 | 12 |
| β-strand | 157-162 | 6 | 12 |
Chain H: 4 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-16 | 13 | 36 |
| β-strand | 23-30 | 8 | 36 |
| β-strand | 37-43 | 7 | 36 |
| β-strand | 54-60 | 7 | 36 |
| α-helix | 67-68 | 2 | |
| α-helix | 78-79 | 2 | |
| α-helix | 89-92 | 4 | |
| β-strand | 95-106 | 12 | 36 |
| β-strand | 111-118 | 8 | 36 |
| β-strand | 121-128 | 8 | 36 |
| α-helix | 129-132 | 4 | |
| β-strand | 139-145 | 7 | 36 |
4 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 |
|---|
| DNA-directed RNA polymerase II subunit RPB3 | C | protein | 318 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P16370 (AlphaFold model) |
| DNA-directed RNA polymerases I, II, and III subunit RPABC1 | E | protein | 215 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P20434 (AlphaFold model) |
| DNA-directed RNA polymerases I, II, and III subunit RPABC2 | F | protein | 155 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P20435 (AlphaFold model) |
| DNA-directed RNA polymerase II subunit RPB7 | G | protein | 171 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P34087 (AlphaFold model) |
| DNA-directed RNA polymerase II subunit RPB9 | I | protein | 122 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P27999 |
| DNA-directed RNA polymerases I, II, and III subunit RPABC5 | J | protein | 70 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P22139 |
| DNA-directed RNA polymerase II subunit RPB11 | K | protein | 120 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P38902 |
| DNA-directed RNA polymerases I, II, and III subunit RPABC4 | L | protein | 70 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P40422 |
| DNA (NTS, non-template strand) | N | DNA | 10 | synthetic construct | |
| RNA (5'-r(*up*ap*up*up*ap*up*gp*ap*gp*gp*gp*gp*ap*ap*a)-3') | P | RNA | 15 | synthetic construct | |
| DNA (TS, template strand) | T | DNA | 20 | synthetic construct | |
| DNA-directed RNA polymerase II subunit RPB1 | A | protein | 1733 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P04050 |
3 more molecules are not listed.
Sequence of entity 1 (C), FASTA
>9W8R_1 DNA-directed RNA polymerase II subunit RPB3 (chains C)
MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLAD
EFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVI
VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEY
DPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPV
DQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPY
SNASQMGNTGSGGYDNAW
Sequence of entity 2 (E), FASTA
>9W8R_2 DNA-directed RNA polymerases I, II, and III subunit RPABC1 (chains E)
MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSF
QANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSA
MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQR
ADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM
Sequence of entity 3 (F), FASTA
>9W8R_3 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQ
HEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRI
AMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL
Sequence of entity 4 (G), FASTA
>9W8R_4 DNA-directed RNA polymerase II subunit RPB7 (chains G)
MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGR
ILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLT
FNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAIGSIKEDYLGAI
Sequence of entity 5 (I), FASTA
>9W8R_5 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQ
DIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQ
FS
Sequence of entity 6 (J), FASTA
>9W8R_6 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKF
LRYNPLEKRD
Sequence of entity 7 (K), FASTA
>9W8R_7 DNA-directed RNA polymerase II subunit RPB11 (chains K)
MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAA
YKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETEWNLQTLAADDAF
Sequence of entity 8 (L), FASTA
>9W8R_8 DNA-directed RNA polymerases I, II, and III subunit RPABC4 (chains L)
MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKAR
TKRLVQFEAR
Sequence of entity 9 (N), FASTA
>9W8R_9 DNA (NTS, non-template strand) (chains N)
GAGAGCGAGG
Sequence of entity 10 (P), FASTA
>9W8R_10 RNA (5'-R(*UP*AP*UP*UP*AP*UP*GP*AP*GP*GP*GP*GP*AP*AP*A)-3') (chains P)
UAUUAUGAGGGGAAA
Sequence of entity 11 (T), FASTA
>9W8R_11 DNA (TS, template strand) (chains T)
CCTCGCTCTCCTTTCCCCTC
Sequence of entity 12 (A), FASTA
>9W8R_12 DNA-directed RNA polymerase II subunit RPB1 (chains A)
MVGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGS
IDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNE
LMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLK
LVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLP
VPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHV
ATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLE
LDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKR
AGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNA
DFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTF
IELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSP
KDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHN
GFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVR
FLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFV
DRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRR
LVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVD
LLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNI
RRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCC
LLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMT
LNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEH
TTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRA
AMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHML
KKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVP
GIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGG
LTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGA
FDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGS
NDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTS
PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS
PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSP
SYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 1 |
| ZN | Zinc ion | Zn | 8 |
Primary citation
Structure of yeast Pol II in complex with a short control scaffold lacking cisplatin-ICL lesion. Xu, J., Zhu, L. To be published.
Other PDB entries of the same protein (UniProt P16370 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9SV6 1.96 Å, CryoEM structure of transcribing RNA polymerase II elongation complex with ATP and Elf1
- 9W8V 2.23 Å, Structure of post-translocation state of yeast Pol II complexed with a cisplatin-induced…
- 9QEB 2.26 Å, CryoEM structure of transcribing RNA polymerase II elongation complex
- 1TWF 2.3 Å, RNA polymerase II complexed with UTP at 2.3 A resolution
- 9RYB 2.33 Å, CryoEM structure of transcribing RNA polymerase II elongation complex in post-catalysis…
- 9KD8 2.46 Å, The structure of RNA polymerase II elongation complex paused at N-2 state by actinomycin…
- 9K7F 2.5 Å, RNA polymerase II elongation complex apo structure.
- 30ES 2.54 Å, Cryo-EM structure of the yeast RNA polymerase II elongation complex with 19-mer RNA in…
- 30EP 2.55 Å, Cryo-EM structure of the yeast RNA polymerase II elongation complex with 19-mer RNA in…
- 9W8T 2.56 Å, Structure of yeast Pol II in complex with a cisplatin-induced inter-strand crosslink…
- 9W8U 2.61 Å, Structure of pre-translocation state of yeast Pol II complexed with a cisplatin-induced…
- 9KDQ 2.63 Å, The structure of 3 ACTD bound to RNA polymerase II elongation complex with 4 CTG repeats.
Browse structure collections
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