9FYX: RNA polymerase II subunit D
Influenza A/H7N9 polymerase pre-cleavage cap-snatching complex. Determined by electron microscopy at 3.3 Å resolution. Released 16 Jul 2025.
- Method
- Electron microscopy
- Resolution
- 3.3 Å
- Organisms
- Sus scrofa domesticus, synthetic construct, Influenza B virus
- Chains
- 23
- Atoms
- 56,176
- Mol. weight
- 925.2 kDa
- Ligands
- ZN, G1G, MG, PO4
- Released
- 16 Jul 2025
Explore 9FYX in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9FYX contains 322 α-helices and 388 β-strands across 17 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: 35 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-7 | 6 | |
| α-helix | 11-24 | 14 | |
| α-helix | 32-48 | 17 | |
| β-strand | 53-54 | 2 | 90 |
| β-strand | 73-74 | 2 | 90 |
| β-strand | 76-78 | 3 | 91 |
| α-helix | 84-98 | 15 | |
| β-strand | 109-111 | 3 | 91 |
| β-strand | 116-123 | 8 | 91 |
| α-helix | 127-138 | 12 | |
| β-strand | 144-149 | 6 | 91 |
| β-strand | 154-156 | 3 | 91 |
| α-helix | 157-159 | 3 | |
| α-helix | 165-185 | 21 | |
| α-helix | 188-191 | 4 | |
| α-helix | 210-217 | 8 | |
| α-helix | 226-234 | 9 | |
| α-helix | 241-248 | 8 | |
| α-helix | 256-257 | 2 | |
| β-strand | 258-259 | 2 | 92 |
| α-helix | 265-271 | 7 | |
| β-strand | 275 | 1 | 93 |
| α-helix | 276 | 1 | |
| β-strand | 287 | 1 | 94 |
| β-strand | 290-292 | 3 | 94 |
| α-helix | 303-311 | 9 | |
| β-strand | 317-324 | 8 | 94 |
| α-helix | 331-350 | 20 | |
| β-strand | 359-360 | 2 | 94 |
| α-helix | 364-369 | 6 | |
| α-helix | 376 | 1 | |
| β-strand | 377-378 | 2 | 95 |
| α-helix | 381-383 | 3 | |
| β-strand | 391-392 | 2 | 95 |
| α-helix | 393-394 | 2 | |
| α-helix | 396-398 | 3 | |
| β-strand | 402 | 1 | 93 |
| α-helix | 405-414 | 10 | |
| β-strand | 417 | 1 | 96 |
| β-strand | 421 | 1 | 97 |
| α-helix | 425-431 | 7 | |
| α-helix | 434-451 | 18 | |
| β-strand | 453 | 1 | 96 |
| α-helix | 454-475 | 22 | |
| β-strand | 480-488 | 9 | 94 |
| β-strand | 490 | 1 | 97 |
| β-strand | 498-506 | 9 | 94 |
| β-strand | 517-526 | 10 | 94 |
| α-helix | 530-532 | 3 | |
| α-helix | 534-537 | 4 | |
| β-strand | 541-551 | 11 | 94 |
| β-strand | 556-571 | 16 | 94 |
| α-helix | 572-579 | 8 | |
| α-helix | 583-603 | 21 | |
| α-helix | 608-609 | 2 | |
| α-helix | 610-614 | 5 | |
| β-strand | 619-624 | 6 | 98 |
| β-strand | 627-631 | 5 | 98 |
| α-helix | 633-649 | 17 | |
| α-helix | 653-673 | 21 | |
| β-strand | 679-680 | 2 | 92 |
| α-helix | 683-691 | 9 | |
| α-helix | 698-714 | 17 | |
Chain A: 82 helices, 76 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14 | 1 | |
| β-strand | 15 | 1 | 34 |
| β-strand | 20-22 | 3 | 35 |
| β-strand | 25 | 1 | 36 |
| α-helix | 28-34 | 7 | |
| β-strand | 43 | 1 | 37 |
| β-strand | 47-48 | 2 | 38 |
| β-strand | 51-52 | 2 | 38 |
| α-helix | 53 | 1 | |
| β-strand | 56 | 1 | 37 |
| α-helix | 60-62 | 3 | |
| α-helix | 82-85 | 4 | |
| β-strand | 86-94 | 9 | 39 |
| α-helix | 97-99 | 3 | |
| α-helix | 100-109 | 10 | |
| β-strand | 110 | 1 | 40 |
| β-strand | 117 | 1 | 40 |
| α-helix | 124-132 | 9 | |
| α-helix | 137-148 | 12 | |
| β-strand | 153 | 1 | 41 |
| β-strand | 187 | 1 | 41 |
| α-helix | 188-189 | 2 | |
| β-strand | 190-194 | 5 | 42 |
| β-strand | 197-201 | 5 | 42 |
| β-strand | 213-216 | 4 | 42 |
| α-helix | 218-227 | 10 | |
| α-helix | 230-235 | 6 | |
| α-helix | 246-248 | 3 | |
| β-strand | 250-255 | 6 | 39 |
| α-helix | 256 | 1 | |
| β-strand | 265 | 1 | 43 |
| β-strand | 271 | 1 | 43 |
| α-helix | 272-274 | 3 | |
| α-helix | 275-295 | 21 | |
| α-helix | 301-318 | 18 | |
| α-helix | 326-327 | 2 | |
| β-strand | 329 | 1 | 44 |
| α-helix | 331-333 | 3 | |
| α-helix | 334 | 1 | |
| β-strand | 335 | 1 | 44 |
| α-helix | 336 | 1 | |
| α-helix | 339-342 | 4 | |
| α-helix | 350-354 | 5 | |
| β-strand | 357-359 | 3 | 45 |
| β-strand | 362-369 | 8 | 46 |
| β-strand | 377-379 | 3 | 46 |
| β-strand | 381 | 1 | 47 |
| α-helix | 382-387 | 6 | |
| β-strand | 389-393 | 5 | 48 |
| α-helix | 394 | 1 | |
| α-helix | 399-408 | 10 | |
| β-strand | 416-420 | 5 | 48 |
| β-strand | 426-428 | 3 | 48 |
| α-helix | 435-438 | 4 | |
| β-strand | 445-449 | 5 | 48 |
| α-helix | 450 | 1 | |
| β-strand | 455-459 | 5 | 46 |
| α-helix | 466-468 | 3 | |
| β-strand | 469-474 | 6 | 46 |
| β-strand | 477 | 1 | 47 |
| β-strand | 482-484 | 3 | 46 |
| α-helix | 487-489 | 3 | |
| β-strand | 500-504 | 5 | 46 |
| α-helix | 509-514 | 6 | |
| α-helix | 515-519 | 5 | |
| β-strand | 520 | 1 | 46 |
| α-helix | 522-524 | 3 | |
| β-strand | 526-527 | 2 | 49 |
| β-strand | 532-533 | 2 | 49 |
| α-helix | 539-548 | 10 | |
| β-strand | 554-555 | 2 | 50 |
| α-helix | 557-565 | 9 | |
| α-helix | 574 | 1 | |
| β-strand | 575 | 1 | 12 |
| α-helix | 576-577 | 2 | |
| β-strand | 579-581 | 3 | 13 |
| β-strand | 585 | 1 | 13 |
| β-strand | 586-587 | 2 | 50 |
| α-helix | 588-595 | 8 | |
| β-strand | 602-604 | 3 | 51 |
| β-strand | 628-631 | 4 | 51 |
| β-strand | 634-637 | 4 | 51 |
| α-helix | 642-645 | 4 | |
| α-helix | 652-659 | 8 | |
| α-helix | 662-683 | 22 | |
| β-strand | 686 | 1 | 52 |
| α-helix | 689-692 | 4 | |
| α-helix | 696-721 | 26 | |
| α-helix | 726-728 | 3 | |
| α-helix | 733-759 | 27 | |
| α-helix | 765-772 | 8 | |
| α-helix | 778-785 | 8 | |
| β-strand | 789-790 | 2 | 53 |
| β-strand | 792-793 | 2 | 54 |
| β-strand | 796-797 | 2 | 54 |
| α-helix | 798-799 | 2 | |
| β-strand | 822-823 | 2 | 53 |
| α-helix | 833-868 | 36 | |
| β-strand | 872-873 | 2 | 55 |
| β-strand | 879-880 | 2 | 55 |
| β-strand | 886-888 | 3 | 55 |
| α-helix | 891-893 | 3 | |
| β-strand | 896 | 1 | 56 |
| β-strand | 902-905 | 4 | 57 |
| α-helix | 913-920 | 8 | |
| α-helix | 927-933 | 7 | |
| β-strand | 934 | 1 | 58 |
| α-helix | 936-944 | 9 | |
| α-helix | 946-969 | 24 | |
| β-strand | 976-979 | 4 | 57 |
| α-helix | 983-993 | 11 | |
| β-strand | 1002 | 1 | 58 |
| α-helix | 1006-1019 | 14 | |
| α-helix | 1028-1048 | 21 | |
| α-helix | 1051-1056 | 6 | |
| α-helix | 1062-1079 | 18 | |
| β-strand | 1080 | 1 | 56 |
| α-helix | 1081-1082 | 2 | |
| α-helix | 1087-1101 | 15 | |
| α-helix | 1121-1129 | 9 | |
| β-strand | 1139-1142 | 4 | 59 |
| β-strand | 1143 | 1 | 60 |
| α-helix | 1146-1149 | 4 | |
| α-helix | 1152-1161 | 10 | |
| β-strand | 1162 | 1 | 61 |
| β-strand | 1164-1165 | 2 | 62 |
| α-helix | 1166-1169 | 4 | |
| β-strand | 1170-1177 | 8 | 16 |
| α-helix | 1181-1183 | 3 | |
| α-helix | 1190-1197 | 8 | |
| β-strand | 1210-1216 | 7 | 16 |
| α-helix | 1218-1223 | 6 | |
| α-helix | 1228-1239 | 12 | |
| β-strand | 1243-1247 | 5 | 16 |
| β-strand | 1256-1261 | 6 | 16 |
| α-helix | 1281-1295 | 15 | |
| β-strand | 1297-1299 | 3 | 62 |
| β-strand | 1301 | 1 | 61 |
| β-strand | 1307-1310 | 4 | 59 |
| α-helix | 1315-1317 | 3 | |
| β-strand | 1319-1322 | 4 | 63 |
| β-strand | 1328-1331 | 4 | 63 |
| β-strand | 1335-1338 | 4 | 59 |
| α-helix | 1343-1347 | 5 | |
| β-strand | 1352 | 1 | 60 |
| β-strand | 1358-1359 | 2 | 59 |
| α-helix | 1362-1368 | 7 | |
| α-helix | 1371-1388 | 18 | |
| α-helix | 1395-1405 | 11 | |
| α-helix | 1416-1419 | 4 | |
| α-helix | 1426-1432 | 7 | |
| α-helix | 1435-1445 | 11 | |
| β-strand | 1448-1449 | 2 | 35 |
| α-helix | 1454-1459 | 6 | |
| α-helix | 1462-1464 | 3 | |
| α-helix | 1467-1469 | 3 | |
| β-strand | 1471-1475 | 5 | 1 |
| α-helix | 1477-1480 | 4 | |
Chain b: 38 helices, 31 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-3 | 2 | 98 |
| α-helix | 5-10 | 6 | |
| α-helix | 15-21 | 7 | |
| α-helix | 27-30 | 4 | |
| α-helix | 36-48 | 13 | |
| β-strand | 54-57 | 4 | 99 |
| β-strand | 64-67 | 4 | 99 |
| α-helix | 72-74 | 3 | |
| α-helix | 85-98 | 14 | |
| α-helix | 102-116 | 15 | |
| β-strand | 118 | 1 | 100 |
| α-helix | 119-123 | 5 | |
| β-strand | 128-130 | 3 | 101 |
| β-strand | 135-137 | 3 | 101 |
| α-helix | 139-152 | 14 | |
| β-strand | 162 | 1 | 100 |
| α-helix | 163-175 | 13 | |
| β-strand | 178-185 | 8 | 102 |
| β-strand | 206-213 | 8 | 102 |
| α-helix | 214-222 | 9 | |
| β-strand | 223-224 | 2 | 103 |
| β-strand | 225-228 | 4 | 104 |
| β-strand | 240-243 | 4 | 104 |
| α-helix | 246-264 | 19 | |
| β-strand | 269 | 1 | 92 |
| α-helix | 275-292 | 18 | |
| β-strand | 298-305 | 8 | 92 |
| β-strand | 306 | 1 | 105 |
| α-helix | 309-312 | 4 | |
| α-helix | 315-325 | 11 | |
| α-helix | 331-345 | 15 | |
| β-strand | 348-350 | 3 | 103 |
| β-strand | 354-359 | 6 | 95 |
| β-strand | 364-369 | 6 | 95 |
| α-helix | 370-372 | 3 | |
| α-helix | 378-380 | 3 | |
| α-helix | 383-392 | 10 | |
| α-helix | 393-395 | 3 | |
| β-strand | 396-397 | 2 | 103 |
| β-strand | 400-402 | 3 | 103 |
| α-helix | 413-425 | 13 | |
| α-helix | 429-432 | 4 | |
| β-strand | 437-443 | 7 | 92 |
| β-strand | 446-453 | 8 | 92 |
| α-helix | 456-473 | 18 | |
| β-strand | 477 | 1 | 105 |
| β-strand | 483-486 | 4 | 92 |
| β-strand | 489-492 | 4 | 106 |
| β-strand | 495-498 | 4 | 106 |
| β-strand | 501 | 1 | 106 |
| α-helix | 505-508 | 4 | |
| α-helix | 519-535 | 17 | |
| α-helix | 541-559 | 19 | |
| α-helix | 573-582 | 10 | |
| α-helix | 586-588 | 3 | |
| α-helix | 591-593 | 3 | |
| α-helix | 608-611 | 4 | |
| α-helix | 618-624 | 7 | |
| α-helix | 637-639 | 3 | |
| β-strand | 642-645 | 4 | 107 |
| β-strand | 653-656 | 4 | 107 |
| β-strand | 667-668 | 2 | 108 |
| α-helix | 669-671 | 3 | |
| α-helix | 673-676 | 4 | |
| α-helix | 680-699 | 20 | |
| α-helix | 702-705 | 4 | |
| β-strand | 713 | 1 | 109 |
| α-helix | 714-732 | 19 | |
| α-helix | 737-756 | 20 | |
Chain B: 52 helices, 83 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-18 | 3 | |
| α-helix | 19-36 | 18 | |
| α-helix | 41-49 | 9 | |
| α-helix | 50-54 | 5 | |
| α-helix | 55-61 | 7 | |
| α-helix | 63-64 | 2 | |
| β-strand | 67-68 | 2 | 64 |
| β-strand | 83-84 | 2 | 64 |
| β-strand | 87-93 | 7 | 64 |
| β-strand | 97-99 | 3 | 65 |
| β-strand | 105-107 | 3 | 65 |
| α-helix | 110-116 | 7 | |
| β-strand | 121-133 | 13 | 64 |
| β-strand | 139-153 | 15 | 64 |
| α-helix | 168-173 | 6 | |
| β-strand | 185-187 | 3 | 66 |
| β-strand | 190-193 | 4 | 66 |
| α-helix | 194-195 | 2 | |
| β-strand | 196-200 | 5 | 67 |
| β-strand | 205-208 | 4 | 68 |
| β-strand | 215-223 | 9 | 68 |
| β-strand | 233-240 | 8 | 68 |
| β-strand | 256-259 | 4 | 68 |
| β-strand | 263 | 1 | 69 |
| β-strand | 267-268 | 2 | 68 |
| α-helix | 269-275 | 7 | |
| α-helix | 281-288 | 8 | |
| α-helix | 295-307 | 13 | |
| α-helix | 314-324 | 11 | |
| β-strand | 325 | 1 | 69 |
| α-helix | 332-345 | 14 | |
| α-helix | 349-351 | 3 | |
| α-helix | 358-376 | 19 | |
| α-helix | 381-384 | 4 | |
| α-helix | 388-390 | 3 | |
| β-strand | 391-394 | 4 | 67 |
| α-helix | 396-423 | 28 | |
| α-helix | 431-434 | 4 | |
| α-helix | 437-450 | 14 | |
| β-strand | 453 | 1 | 70 |
| β-strand | 463 | 1 | 70 |
| β-strand | 468-469 | 2 | 66 |
| α-helix | 470-471 | 2 | |
| α-helix | 475-482 | 8 | |
| β-strand | 484 | 1 | 71 |
| β-strand | 485-486 | 2 | 67 |
| α-helix | 503-505 | 3 | |
| β-strand | 509 | 1 | 72 |
| β-strand | 525 | 1 | 71 |
| β-strand | 526 | 1 | 72 |
| β-strand | 531-532 | 2 | 73 |
| α-helix | 539-547 | 9 | |
| β-strand | 551-552 | 2 | 74 |
| α-helix | 558-561 | 4 | |
| β-strand | 565-569 | 5 | 74 |
| β-strand | 572-577 | 6 | 74 |
| α-helix | 580-592 | 13 | |
| β-strand | 602-606 | 5 | 74 |
| β-strand | 611-615 | 5 | 74 |
| β-strand | 621-627 | 7 | 73 |
| β-strand | 628 | 1 | 75 |
| β-strand | 633 | 1 | 75 |
| α-helix | 637-644 | 8 | |
| α-helix | 653-658 | 6 | |
| β-strand | 662-666 | 5 | 73 |
| α-helix | 667-670 | 4 | |
| β-strand | 675-676 | 2 | 73 |
| α-helix | 679-682 | 4 | |
| β-strand | 695-696 | 2 | 73 |
| α-helix | 700-703 | 4 | |
| α-helix | 706-709 | 4 | |
| α-helix | 714-716 | 3 | |
| β-strand | 717 | 1 | 76 |
| α-helix | 719-728 | 10 | |
| β-strand | 732 | 1 | 77 |
| β-strand | 734 | 1 | 21 |
| β-strand | 747-751 | 5 | 21 |
| β-strand | 755 | 1 | 19 |
| β-strand | 759-760 | 2 | 78 |
| α-helix | 764-767 | 4 | |
| β-strand | 776-782 | 7 | 79 |
| β-strand | 783 | 1 | 52 |
| β-strand | 793-797 | 5 | 79 |
| α-helix | 798-802 | 5 | |
| β-strand | 808-817 | 10 | 21 |
| β-strand | 827-829 | 3 | 80 |
| β-strand | 848 | 1 | 81 |
| β-strand | 853 | 1 | 82 |
| β-strand | 854 | 1 | 81 |
| α-helix | 855 | 1 | |
| β-strand | 859-860 | 2 | 21 |
| β-strand | 865-867 | 3 | 82 |
| β-strand | 869-872 | 4 | 80 |
| β-strand | 889-891 | 3 | 80 |
| α-helix | 893 | 1 | |
| β-strand | 894-895 | 2 | 82 |
| α-helix | 896-897 | 2 | |
| β-strand | 902-911 | 10 | 21 |
| β-strand | 917-927 | 11 | 21 |
| β-strand | 934-937 | 4 | 79 |
| β-strand | 942-949 | 8 | 79 |
| β-strand | 956 | 1 | 83 |
| β-strand | 965-967 | 3 | 79 |
| α-helix | 969-971 | 3 | |
| β-strand | 977 | 1 | 76 |
| α-helix | 978-993 | 16 | |
| β-strand | 997-998 | 2 | 78 |
| α-helix | 1008-1016 | 9 | |
| β-strand | 1025-1026 | 2 | 79 |
| β-strand | 1029 | 1 | 83 |
| α-helix | 1035 | 1 | |
| β-strand | 1036 | 1 | 83 |
| α-helix | 1037 | 1 | |
| β-strand | 1041-1050 | 10 | 79 |
| β-strand | 1051 | 1 | 77 |
| β-strand | 1060-1062 | 3 | 46 |
| β-strand | 1067 | 1 | 84 |
| β-strand | 1074 | 1 | 84 |
| α-helix | 1082-1083 | 2 | |
| β-strand | 1084-1086 | 3 | 45 |
| α-helix | 1088-1097 | 10 | |
| α-helix | 1100-1104 | 5 | |
| α-helix | 1105-1109 | 5 | |
| β-strand | 1113-1119 | 7 | 34 |
| α-helix | 1124 | 1 | |
| β-strand | 1125 | 1 | 34 |
| α-helix | 1126 | 1 | |
| β-strand | 1127-1129 | 3 | 85 |
| β-strand | 1134-1136 | 3 | 85 |
| β-strand | 1137 | 1 | 86 |
| β-strand | 1142 | 1 | 86 |
| β-strand | 1146-1152 | 7 | 34 |
| α-helix | 1153-1164 | 12 | |
| β-strand | 1167 | 1 | 36 |
| β-strand | 1170-1172 | 3 | 35 |
Chain c: 38 helices, 42 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-12 | 11 | |
| α-helix | 14-22 | 9 | |
| β-strand | 24 | 1 | 109 |
| α-helix | 25-31 | 7 | |
| α-helix | 43-50 | 8 | |
| β-strand | 57-59 | 3 | 108 |
| α-helix | 63-66 | 4 | |
| β-strand | 70 | 1 | 110 |
| β-strand | 76 | 1 | 110 |
| β-strand | 78-82 | 5 | 108 |
| α-helix | 83 | 1 | |
| α-helix | 88 | 1 | |
| β-strand | 89-91 | 3 | 108 |
| α-helix | 93-102 | 10 | |
| α-helix | 111-114 | 4 | |
| α-helix | 116-126 | 11 | |
| β-strand | 129-135 | 7 | 111 |
| β-strand | 141-148 | 8 | 112 |
| α-helix | 156-167 | 12 | |
| α-helix | 170-172 | 3 | |
| α-helix | 180-192 | 13 | |
| α-helix | 200-211 | 12 | |
| β-strand | 214-220 | 7 | 112 |
| α-helix | 226-229 | 4 | |
| α-helix | 232-235 | 4 | |
| β-strand | 236 | 1 | 111 |
| β-strand | 240-245 | 6 | 111 |
| α-helix | 252-271 | 20 | |
| α-helix | 276-286 | 11 | |
| β-strand | 287-289 | 3 | 113 |
| β-strand | 292-293 | 2 | 113 |
| α-helix | 295-298 | 4 | |
| α-helix | 306-314 | 9 | |
| β-strand | 319 | 1 | 114 |
| β-strand | 322-325 | 4 | 115 |
| β-strand | 328-335 | 8 | 115 |
| β-strand | 338-345 | 8 | 116 |
| β-strand | 351-358 | 8 | 116 |
| β-strand | 361-366 | 6 | 115 |
| β-strand | 371-377 | 7 | 115 |
| β-strand | 380-386 | 7 | 115 |
| α-helix | 391-405 | 15 | |
| α-helix | 408-412 | 5 | |
| β-strand | 421 | 1 | 117 |
| α-helix | 426 | 1 | |
| β-strand | 427 | 1 | 117 |
| α-helix | 428-429 | 2 | |
| α-helix | 430-440 | 11 | |
| α-helix | 443-447 | 5 | |
| β-strand | 451-453 | 3 | 118 |
| β-strand | 462-463 | 2 | 119 |
| β-strand | 469-470 | 2 | 119 |
| β-strand | 473-475 | 3 | 118 |
| β-strand | 478-480 | 3 | 115 |
| β-strand | 494 | 1 | 114 |
| β-strand | 497-498 | 2 | 120 |
| β-strand | 504-505 | 2 | 120 |
| β-strand | 511-513 | 3 | 120 |
| α-helix | 515-517 | 3 | |
| β-strand | 529-531 | 3 | 113 |
| α-helix | 542-555 | 14 | |
| α-helix | 557-566 | 10 | |
| α-helix | 568-573 | 6 | |
| α-helix | 575-577 | 3 | |
| α-helix | 578-583 | 6 | |
| α-helix | 586-605 | 20 | |
| α-helix | 612-618 | 7 | |
| α-helix | 619-622 | 4 | |
| α-helix | 625-626 | 2 | |
| β-strand | 635-640 | 6 | 121 |
| β-strand | 643-648 | 6 | 121 |
| β-strand | 653 | 1 | 122 |
| β-strand | 656-659 | 4 | 122 |
| β-strand | 664-667 | 4 | 122 |
| β-strand | 670-674 | 5 | 122 |
| α-helix | 675-677 | 3 | |
| β-strand | 694-699 | 6 | 123 |
| α-helix | 712-715 | 4 | |
| β-strand | 721-725 | 5 | 123 |
| β-strand | 731-736 | 6 | 123 |
Chain C: 11 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8-14 | 7 | 87 |
| β-strand | 18-24 | 7 | 87 |
| α-helix | 28-40 | 13 | |
| β-strand | 44-55 | 12 | 22 |
| α-helix | 61-69 | 9 | |
| β-strand | 72 | 1 | 22 |
| β-strand | 73 | 1 | 88 |
| β-strand | 99-106 | 8 | 22 |
| α-helix | 112 | 1 | |
| β-strand | 113-116 | 4 | 89 |
| α-helix | 117-119 | 3 | |
| β-strand | 121-122 | 2 | 22 |
| β-strand | 129 | 1 | 88 |
| α-helix | 130-132 | 3 | |
| α-helix | 147-148 | 2 | |
| β-strand | 149-153 | 5 | 89 |
| β-strand | 158-168 | 11 | 22 |
| α-helix | 174-176 | 3 | |
| β-strand | 179-185 | 7 | 87 |
| α-helix | 200-202 | 3 | |
| α-helix | 204-206 | 3 | |
| α-helix | 218-220 | 3 | |
| β-strand | 229-235 | 7 | 87 |
| α-helix | 241-270 | 30 | |
Chain D: 9 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 24-26 | 3 | |
| β-strand | 30-31 | 2 | 1 |
| α-helix | 34-49 | 16 | |
| α-helix | 55-58 | 4 | |
| α-helix | 59-70 | 12 | |
| α-helix | 77-89 | 13 | |
| α-helix | 94-103 | 10 | |
| α-helix | 108-114 | 7 | |
| α-helix | 116-118 | 3 | |
| α-helix | 124-136 | 13 | |
Chain E: 12 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-24 | 21 | |
| β-strand | 26-27 | 2 | 2 |
| α-helix | 30-33 | 4 | |
| α-helix | 37-44 | 8 | |
| β-strand | 47 | 1 | 3 |
| β-strand | 52 | 1 | 3 |
| α-helix | 55-58 | 4 | |
| β-strand | 60-64 | 5 | 2 |
| β-strand | 71-75 | 5 | 2 |
| β-strand | 81-82 | 2 | 4 |
| α-helix | 84-97 | 14 | |
| β-strand | 101-106 | 6 | 2 |
| β-strand | 109-110 | 2 | 4 |
| α-helix | 112-120 | 9 | |
| β-strand | 126-131 | 6 | 2 |
| α-helix | 132-135 | 4 | |
| α-helix | 139-141 | 3 | |
| β-strand | 147-150 | 4 | 5 |
| α-helix | 151-152 | 2 | |
| α-helix | 153-163 | 11 | |
| α-helix | 167-169 | 3 | |
| β-strand | 172-173 | 2 | 5 |
| α-helix | 178-183 | 6 | |
| β-strand | 190-197 | 8 | 5 |
| β-strand | 201-209 | 9 | 5 |
9 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 |
|---|
| RNA polymerase II subunit D | D | protein | 184 | Sus scrofa domesticus | A0A287ADR4 (AlphaFold model) |
| DNA-directed RNA polymerase II subunit E | E | protein | 210 | Sus scrofa domesticus | I3LSI7 (AlphaFold model) |
| DNA-directed RNA polymerases I, II, and III subunit RPABC2 | F | protein | 127 | Sus scrofa domesticus | A0A4X1VEK9 (AlphaFold model) |
| DNA-directed RNA polymerase subunit | G | protein | 171 | Sus scrofa domesticus | A0A4X1VKG7 (AlphaFold model) |
| DNA-directed RNA polymerases I, II, and III subunit RPABC3 | H | protein | 150 | Sus scrofa domesticus | I3LCB2 |
| DNA-directed RNA polymerase II subunit RPB9 | I | protein | 125 | Sus scrofa domesticus | P60899 |
| DNA-directed RNA polymerases I, II, and III subunit RPABC5 | J | protein | 67 | Sus scrofa domesticus | A0A4X1VYD0 |
| DNA-directed RNA polymerase II subunit RPB11-a | K | protein | 117 | Sus scrofa domesticus | F1RKE4 |
| RNA polymerase II, I and III subunit K | L | protein | 58 | Sus scrofa domesticus | A0A4X1TRS6 |
| non-template DNA (43-mer) | N | DNA | 43 | synthetic construct | |
| cap(1)-RNA (35-MER) | P | RNA | 35 | Influenza B virus | |
| Template DNA (43-MER) | T | DNA | 43 | synthetic construct | |
11 more molecules are not listed.
Sequence of entity 1 (D), FASTA
>9FYX_1 RNA polymerase II subunit D (chains D)
MWGPAQPYSDSALSPKPRPFRAVFRGSALPFPAVRVEVRGRSMAAGGSDPRAGDVEEDAS
QLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRE
TIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDIQTKR
SFQY
Sequence of entity 2 (E), FASTA
>9FYX_2 DNA-directed RNA polymerase II subunit E (chains E)
MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTV
LVAHNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVD
MAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVA
RYFGIKRGQVVKIIRPSETAGRYITYRLVQ
Sequence of entity 3 (F), FASTA
>9FYX_3 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKY
ERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGV
DELIISD
Sequence of entity 4 (G), FASTA
>9FYX_4 DNA-directed RNA polymerase subunit (chains G)
MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQ
PGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFD
PNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAIGSLMDDYLGLV
Sequence of entity 5 (H), FASTA
>9FYX_5 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVI
ASTLYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGG
LLMRLQGDANNLHGFEVDSRVYLLMKKLAF
Sequence of entity 6 (I), FASTA
>9FYX_6 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MEPDGTYEPGFVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITH
EVDELTQIIADVSQDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCG
HRWTE
Sequence of entity 7 (J), FASTA
>9FYX_7 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL
NYAPLEK
Sequence of entity 8 (K), FASTA
>9FYX_8 DNA-directed RNA polymerase II subunit RPB11-a (chains K)
MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG
YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVAIKDKQEGIE
Sequence of entity 9 (L), FASTA
>9FYX_9 RNA polymerase II, I and III subunit K (chains L)
MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR
Sequence of entity 10 (N), FASTA
>9FYX_10 non-template DNA (43-mer) (chains N)
GGCAGTACTAGTATTCTAGTATTGAAAGTACTTGAGCTTGATC
Sequence of entity 11 (P), FASTA
>9FYX_11 cap(1)-RNA (35-MER) (chains P)
GAAGCGAGAAGAACACAGACAGCAGAAGACCAGGC
Sequence of entity 12 (T), FASTA
>9FYX_12 Template DNA (43-MER) (chains T)
GATCAAGCTCAAGTACTTAAGCCTGGTCTATACTAGTACTGCC
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 9 |
| G1G | 7-methyl-guanosine-5'-triphosphate-5'-(2'-O-methyl)-guanosine | C22 H32 N10 O18 P3 | 1 |
| MG | Magnesium ion | Mg | 2 |
| PO4 | Phosphate ion | O4 P | 2 |
Primary citation
Mechanism of co-transcriptional cap snatching by influenza polymerase. Rotsch, A.H., Li, D., Dupont, M. et al. Nature (2026) 652:1281-1288. DOI 10.1038/s41586-026-10189-0 · PubMed
Other PDB entries of the same protein (UniProt A0A287ADR4 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9BZ0 1.9 Å, Structure of an STK19-containing TC-NER complex
- 7NVU 2.5 Å, RNA polymerase II core pre-initiation complex with open promoter DNA
- 7OOB 2.7 Å, Pol II-CSB-CSA-DDB1-UVSSA-ADPBeF3 (Structure2)
- 7F4G 2.78 Å, Structure of RPAP2-bound RNA polymerase II
- 7NVS 2.8 Å, RNA polymerase II core pre-initiation complex with closed promoter DNA in proximal…
- 7OO3 2.8 Å, Pol II-CSB-CSA-DDB1-UVSSA (Structure1)
- 8OEW 2.8 Å, Structure of the mammalian Pol II-Elongin complex, lacking the ELOA latch (composite…
- 8UHD 2.8 Å, Structure of paused transcription complex Pol II-DSIF-NELF - post-translocated
- 8OEV 2.86 Å, Structure of the mammalian Pol II-SPT6-Elongin complex, lacking ELOA latch (composite…
- 7NVT 2.9 Å, RNA polymerase II core pre-initiation complex with closed promoter DNA in distal position
- 7OOP 2.9 Å, Pol II-CSB-CSA-DDB1-UVSSA-PAF-SPT6 (Structure 3)
- 8S52 2.9 Å, RNA polymerase II core initially transcribing complex with an ordered RNA of 10 nt
Browse structure collections
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