7O4I: PDB entry 7O4I
Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble. Determined by electron microscopy at 3.2 Å resolution. Released 16 Jun 2021.
- Method
- Electron microscopy
- Resolution
- 3.2 Å
- Organisms
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c), synthetic construct
- Chains
- 30
- Atoms
- 73,949
- Mol. weight
- 1363.82 kDa
- Ligands
- ADP, MG, BEF, ZN
- Released
- 16 Jun 2021
Explore 7O4I in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7O4I contains 447 α-helices and 435 β-strands across 28 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 0: 43 helices, 27 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 1 |
| β-strand | 9-11 | 3 | 1 |
| β-strand | 17 | 1 | 2 |
| α-helix | 19-34 | 16 | |
| β-strand | 37-41 | 5 | 3 |
| α-helix | 49-62 | 14 | |
| β-strand | 69-73 | 5 | 3 |
| α-helix | 76-97 | 22 | |
| β-strand | 104-107 | 4 | 3 |
| α-helix | 126-137 | 12 | |
| α-helix | 140-147 | 8 | |
| α-helix | 157-164 | 8 | |
| α-helix | 167-169 | 3 | |
| β-strand | 174-176 | 3 | 3 |
| α-helix | 178-188 | 11 | |
| α-helix | 192-199 | 8 | |
| β-strand | 205-209 | 5 | 3 |
| α-helix | 211-214 | 4 | |
| α-helix | 216-223 | 8 | |
| β-strand | 231-235 | 5 | 3 |
| α-helix | 237-239 | 3 | |
| α-helix | 240-247 | 8 | |
| β-strand | 250-253 | 4 | 4 |
| α-helix | 254-277 | 24 | |
| α-helix | 280-291 | 12 | |
| α-helix | 295-298 | 4 | |
| α-helix | 313-315 | 3 | |
| α-helix | 320-321 | 2 | |
| α-helix | 328-345 | 18 | |
| β-strand | 352-354 | 3 | 4 |
| α-helix | 356-366 | 11 | |
| α-helix | 371-375 | 5 | |
| α-helix | 377-387 | 11 | |
| α-helix | 395-398 | 4 | |
| α-helix | 399-409 | 11 | |
| β-strand | 416-421 | 6 | 4 |
| β-strand | 423 | 1 | 5 |
| β-strand | 432 | 1 | 5 |
| β-strand | 434-439 | 6 | 4 |
| α-helix | 447-452 | 6 | |
| β-strand | 456-460 | 5 | 3 |
| α-helix | 468-472 | 5 | |
| β-strand | 477-482 | 6 | 3 |
| β-strand | 492-497 | 6 | 6 |
| β-strand | 499 | 1 | 7 |
| β-strand | 505 | 1 | 7 |
| α-helix | 510-512 | 3 | |
| α-helix | 516-532 | 17 | |
| β-strand | 536-541 | 6 | 6 |
| α-helix | 544-557 | 14 | |
| α-helix | 559-566 | 8 | |
| β-strand | 568-571 | 4 | 6 |
| α-helix | 576-591 | 16 | |
| β-strand | 596-601 | 6 | 6 |
| α-helix | 606-608 | 3 | |
| β-strand | 619-623 | 5 | 6 |
| α-helix | 633-645 | 13 | |
| α-helix | 650-666 | 17 | |
| α-helix | 667-669 | 3 | |
| β-strand | 677-682 | 6 | 6 |
| α-helix | 684-688 | 5 | |
| α-helix | 690-692 | 3 | |
| α-helix | 695-700 | 6 | |
| α-helix | 703-705 | 3 | |
| β-strand | 708 | 1 | 6 |
| α-helix | 710-724 | 15 | |
| α-helix | 727-729 | 3 | |
| α-helix | 730-733 | 4 | |
| β-strand | 739 | 1 | 2 |
| α-helix | 741-751 | 11 | |
Chain 1: 37 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-9 | 6 | 9 |
| β-strand | 12-19 | 8 | 9 |
| α-helix | 25 | 1 | |
| β-strand | 26-31 | 6 | 9 |
| β-strand | 37-41 | 5 | 9 |
| α-helix | 42-44 | 3 | |
| β-strand | 45-50 | 6 | 9 |
| β-strand | 59-64 | 6 | 9 |
| α-helix | 65 | 1 | |
| β-strand | 86-90 | 5 | 9 |
| α-helix | 94-120 | 27 | |
| α-helix | 171-176 | 6 | |
| α-helix | 178-187 | 10 | |
| α-helix | 189-195 | 7 | |
| α-helix | 196-201 | 6 | |
| α-helix | 206-211 | 6 | |
| α-helix | 214-224 | 11 | |
| α-helix | 228-230 | 3 | |
| α-helix | 233-236 | 4 | |
| β-strand | 246-251 | 6 | 10 |
| α-helix | 253-262 | 10 | |
| α-helix | 264-271 | 8 | |
| α-helix | 280-289 | 10 | |
| α-helix | 291-296 | 6 | |
| α-helix | 309-312 | 4 | |
| α-helix | 315-329 | 15 | |
| α-helix | 335-337 | 3 | |
| α-helix | 339-344 | 6 | |
| α-helix | 353-355 | 3 | |
| α-helix | 356-358 | 3 | |
| β-strand | 362 | 1 | 11 |
| β-strand | 368 | 1 | 11 |
| α-helix | 371-389 | 19 | |
| α-helix | 414-419 | 6 | |
| α-helix | 422-424 | 3 | |
| α-helix | 426-428 | 3 | |
| β-strand | 432 | 1 | 12 |
| α-helix | 433 | 1 | |
| β-strand | 434 | 1 | 13 |
| α-helix | 442-444 | 3 | |
| α-helix | 466-482 | 17 | |
| α-helix | 486-489 | 4 | |
| α-helix | 496-514 | 19 | |
| α-helix | 537-539 | 3 | |
| α-helix | 544-568 | 25 | |
| α-helix | 573-575 | 3 | |
| α-helix | 576-604 | 29 | |
| α-helix | 609-615 | 7 | |
| α-helix | 617-638 | 22 | |
Chain 2: 23 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-16 | 11 | |
| α-helix | 19-25 | 7 | |
| α-helix | 29-38 | 10 | |
| α-helix | 41-51 | 11 | |
| β-strand | 57-58 | 2 | 14 |
| α-helix | 59-65 | 7 | |
| β-strand | 66 | 1 | 15 |
| α-helix | 71-83 | 13 | |
| β-strand | 87-92 | 6 | 14 |
| β-strand | 95-100 | 6 | 14 |
| α-helix | 102-113 | 12 | |
| α-helix | 131-136 | 6 | |
| α-helix | 137-151 | 15 | |
| α-helix | 158-160 | 3 | |
| α-helix | 161-169 | 9 | |
| β-strand | 174-176 | 3 | 16 |
| β-strand | 181-183 | 3 | 16 |
| α-helix | 186-193 | 8 | |
| α-helix | 196-210 | 15 | |
| α-helix | 218-230 | 13 | |
| β-strand | 237-238 | 2 | 17 |
| α-helix | 244-254 | 11 | |
| β-strand | 259-261 | 3 | 17 |
| β-strand | 268-271 | 4 | 17 |
| α-helix | 273-279 | 7 | |
| β-strand | 339-341 | 3 | 18 |
| β-strand | 346-349 | 4 | 18 |
| α-helix | 354-361 | 8 | |
| β-strand | 365-370 | 6 | 18 |
| β-strand | 374-377 | 4 | 18 |
| α-helix | 380-388 | 9 | |
| α-helix | 393-402 | 10 | |
| β-strand | 404 | 1 | 18 |
| α-helix | 406-422 | 17 | |
| α-helix | 435-448 | 14 | |
| β-strand | 452-459 | 8 | 19 |
| α-helix | 465-477 | 13 | |
| β-strand | 481-485 | 5 | 19 |
| β-strand | 490-494 | 5 | 19 |
| α-helix | 495-506 | 12 | |
Chain 3: 6 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 12 | 1 | 24 |
| β-strand | 19 | 1 | 24 |
| β-strand | 28-30 | 3 | 25 |
| β-strand | 38-39 | 2 | 25 |
| α-helix | 40-47 | 8 | |
| β-strand | 52-53 | 2 | 26 |
| β-strand | 56 | 1 | 27 |
| β-strand | 59 | 1 | 27 |
| β-strand | 62-63 | 2 | 26 |
| α-helix | 65-67 | 3 | |
| β-strand | 69-70 | 2 | 25 |
| α-helix | 76-89 | 14 | |
| α-helix | 96-99 | 4 | |
| α-helix | 103-122 | 20 | |
| α-helix | 126-138 | 13 | |
Chain 4: 15 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 24-30 | 7 | 30 |
| α-helix | 34-43 | 10 | |
| α-helix | 49-67 | 19 | |
| β-strand | 73-79 | 7 | 30 |
| β-strand | 82-87 | 6 | 30 |
| α-helix | 116-138 | 23 | |
| α-helix | 149-166 | 18 | |
| β-strand | 173-181 | 9 | 30 |
| α-helix | 185-186 | 2 | |
| α-helix | 190-192 | 3 | |
| α-helix | 193-205 | 13 | |
| β-strand | 210-215 | 6 | 30 |
| α-helix | 222-230 | 9 | |
| β-strand | 235-238 | 4 | 30 |
| α-helix | 244-250 | 7 | |
| α-helix | 256-258 | 3 | |
| β-strand | 262 | 1 | 15 |
| β-strand | 275 | 1 | 31 |
| β-strand | 282 | 1 | 31 |
| β-strand | 285-289 | 5 | 32 |
| β-strand | 295-296 | 2 | 32 |
| α-helix | 299-300 | 2 | |
| α-helix | 301-303 | 3 | |
| β-strand | 304 | 1 | 33 |
| β-strand | 311 | 1 | 33 |
| α-helix | 312-313 | 2 | |
| α-helix | 314-321 | 8 | |
| α-helix | 323-325 | 3 | |
Chain 5: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-11 | 5 | 19 |
| α-helix | 14-26 | 13 | |
| β-strand | 31-36 | 6 | 19 |
| β-strand | 39-42 | 4 | 19 |
| α-helix | 44-59 | 16 | |
Chain 6: 19 helices, 23 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 97-113 | 17 | |
| β-strand | 118 | 1 | 13 |
| β-strand | 120 | 1 | 34 |
| β-strand | 124-131 | 8 | 35 |
| α-helix | 134-137 | 4 | |
| α-helix | 145-163 | 19 | |
| β-strand | 168-175 | 8 | 35 |
| β-strand | 178-186 | 9 | 35 |
| α-helix | 189-199 | 11 | |
| α-helix | 203-204 | 2 | |
| α-helix | 210-221 | 12 | |
| β-strand | 229-235 | 7 | 35 |
| α-helix | 247-257 | 11 | |
| β-strand | 260-265 | 6 | 35 |
| α-helix | 271-279 | 9 | |
| β-strand | 288-290 | 3 | 35 |
| α-helix | 294-303 | 10 | |
| α-helix | 307-308 | 2 | |
| β-strand | 309 | 1 | 34 |
| α-helix | 310 | 1 | |
| β-strand | 311 | 1 | 12 |
| β-strand | 319-323 | 5 | 32 |
| β-strand | 326 | 1 | 36 |
| β-strand | 334-335 | 2 | 37 |
| β-strand | 342-343 | 2 | 37 |
| β-strand | 347-348 | 2 | 36 |
| α-helix | 349 | 1 | |
| β-strand | 355-356 | 2 | 36 |
| β-strand | 361-362 | 2 | 32 |
| β-strand | 369-370 | 2 | 32 |
| α-helix | 373-377 | 5 | |
| α-helix | 380-382 | 3 | |
| α-helix | 385-388 | 4 | |
| β-strand | 390-391 | 2 | 38 |
| α-helix | 392-393 | 2 | |
| β-strand | 402 | 1 | 39 |
| β-strand | 409 | 1 | 39 |
| α-helix | 410-411 | 2 | |
| β-strand | 427-428 | 2 | 38 |
| β-strand | 435-436 | 2 | 38 |
| α-helix | 438-446 | 9 | |
| α-helix | 452-456 | 5 | |
Chain 7: 36 helices, 30 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 105-107 | 3 | |
| α-helix | 110-112 | 3 | |
| β-strand | 117-118 | 2 | 18 |
| β-strand | 132-134 | 3 | 40 |
| β-strand | 140-144 | 5 | 40 |
| α-helix | 150-160 | 11 | |
| β-strand | 162-165 | 4 | 40 |
| β-strand | 170-174 | 5 | 40 |
| α-helix | 177-185 | 9 | |
| α-helix | 190-200 | 11 | |
| β-strand | 201 | 1 | 40 |
| α-helix | 204-206 | 3 | |
| α-helix | 207-217 | 11 | |
| β-strand | 224-228 | 5 | 41 |
| β-strand | 231-236 | 6 | 41 |
| α-helix | 242-245 | 4 | |
| β-strand | 314-318 | 5 | 41 |
| α-helix | 323-332 | 10 | |
| α-helix | 335-337 | 3 | |
| β-strand | 338 | 1 | 41 |
| β-strand | 341 | 1 | 42 |
| α-helix | 350-351 | 2 | |
| β-strand | 356 | 1 | 43 |
| α-helix | 364-374 | 11 | |
| β-strand | 379 | 1 | 42 |
| β-strand | 382-384 | 3 | 44 |
| α-helix | 392-403 | 12 | |
| β-strand | 407-410 | 4 | 44 |
| α-helix | 414-427 | 14 | |
| β-strand | 428 | 1 | 43 |
| α-helix | 432-434 | 3 | |
| β-strand | 435-437 | 3 | 44 |
| β-strand | 452-455 | 4 | 44 |
| α-helix | 457-461 | 5 | |
| α-helix | 468-479 | 12 | |
| β-strand | 482 | 1 | 45 |
| β-strand | 484-488 | 5 | 44 |
| α-helix | 490-492 | 3 | |
| α-helix | 499-504 | 6 | |
| β-strand | 507 | 1 | 45 |
| β-strand | 510-513 | 4 | 44 |
| α-helix | 522-526 | 5 | |
| α-helix | 527-530 | 4 | |
| β-strand | 534-536 | 3 | 44 |
| α-helix | 541-546 | 6 | |
| β-strand | 552-559 | 8 | 46 |
| α-helix | 560-562 | 3 | |
| α-helix | 563-571 | 9 | |
| α-helix | 574-582 | 9 | |
| α-helix | 585-600 | 16 | |
| β-strand | 605-609 | 5 | 46 |
| α-helix | 612-622 | 11 | |
| β-strand | 626 | 1 | 46 |
| α-helix | 633-645 | 13 | |
| β-strand | 651-653 | 3 | 46 |
| α-helix | 656-658 | 3 | |
| β-strand | 669-674 | 6 | 46 |
| α-helix | 680-687 | 8 | |
| α-helix | 688-692 | 5 | |
| β-strand | 703-710 | 8 | 46 |
| α-helix | 714-721 | 8 | |
| α-helix | 724-729 | 6 | |
| α-helix | 733 | 1 | |
| β-strand | 734-736 | 3 | 46 |
| α-helix | 753-766 | 14 | |
| α-helix | 832-836 | 5 | |
20 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 |
|---|
| General transcription and DNA repair factor IIH helicase subunit XPD | 0 | protein | 778 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P06839 (AlphaFold model) |
| General transcription and DNA repair factor IIH subunit TFB1 | 1 | protein | 645 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P32776 (AlphaFold model) |
| General transcription and DNA repair factor IIH subunit TFB2 | 2 | protein | 517 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q02939 (AlphaFold model) |
| RNA polymerase II transcription factor B subunit 3 | 3 | protein | 324 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q03290 (AlphaFold model) |
| General transcription and DNA repair factor IIH subunit TFB4 | 4 | protein | 341 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q12004 |
| General transcription and DNA repair factor IIH subunit TFB5 | 5 | protein | 76 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q3E7C1 |
| General transcription and DNA repair factor IIH subunit SSL1 | 6 | protein | 464 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q04673 |
| General transcription and DNA repair factor IIH helicase subunit XPB | 7 | protein | 843 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q00578 |
| DNA-directed RNA polymerase II subunit RPB1 | A | protein | 1733 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P04050 |
| DNA-directed RNA polymerase II subunit RPB2 | B | protein | 1224 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P08518 |
| DNA-directed RNA polymerase II subunit RPB3 | C | protein | 347 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P16370 |
| DNA-directed RNA polymerase II subunit RPB4 | D | protein | 221 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P20433 |
18 more molecules are not listed.
Sequence of entity 1 (0), FASTA
>7O4I_1 General transcription and DNA repair factor IIH helicase subunit XPD (chains 0)
MKFYIDDLPVLFPYPKIYPEQYNYMCDIKKTLDVGGNSILEMPSGTGKTVSLLSLTIAYQ
MHYPEHRKIIYCSRTMSEIEKALVELENLMDYRTKELGYQEDFRGLGLTSRKNLCLHPEV
SKERKGTVVDEKCRRMTNGQAKRKLEEDPEANVELCEYHENLYNIEVEDYLPKGVFSFEK
LLKYCEEKTLCPYFIVRRMISLCNIIIYSYHYLLDPKIAERVSNEVSKDSIVIFDEAHNI
DNVCIESLSLDLTTDALRRATRGANALDERISEVRKVDSQKLQDEYEKLVQGLHSADILT
DQEEPFVETPVLPQDLLTEAIPGNIRRAEHFVSFLKRLIEYLKTRMKVLHVISETPKSFL
QHLKQLTFIERKPLRFCSERLSLLVRTLEVTEVEDFTALKDIATFATLISTYEEGFLLII
EPYEIENAAVPNPIMRFTCLDASIAIKPVFERFSSVIITSGTISPLDMYPRMLNFKTVLQ
KSYAMTLAKKSFLPMIITKGSDQVAISSRFEIRNDPSIVRNYGSMLVEFAKITPDGMVVF
FPSYLYMESIVSMWQTMGILDEVWKHKLILVETPDAQETSLALETYRKACSNGRGAILLS
VARGKVSEGIDFDHQYGRTVLMIGIPFQYTESRILKARLEFMRENYRIRENDFLSFDAMR
HAAQCLGRVLRGKDDYGVMVLADRRFSRKRSQLPKWIAQGLSDADLNLSTDMAISNTKQF
LRTMAQPTDPKDQEGVSVWSYEDLIKHQNSRKDQGGFIENENKEGEQDEDEDEDIEMQ
Sequence of entity 2 (1), FASTA
>7O4I_2 General transcription and DNA repair factor IIH subunit TFB1 (chains 1)
GGSMSHSGAAIFEKVSGIIAINEDVSPAELTWRSTDGDKVHTVVLSTIDKLQATPASSEK
MMLRLIGKVDESKKRKDNEGNEVVPKPQRHMFSFNNRTVMDNIKMTLQQIISRYKDADIY
EEKRRREESAQHTETPMSSSSVTAGTPTPHLDTPQLNNGAPLINTAKLDDSLSKEKLLTN
LKLQQSLLKGNKVLMKVFQETVINAGLPPSEFWSTRIPLLRAFALSTSQKVGPYNVLSTI
KPVASSENKVNVNLSREKILNIFENYPIVKKAYTDNVPKNFKEPEFWARFFSSKLFRKLR
GEKIMQNDRGDVIIDRYLTLDQEFDRKDDDMLLHPVKKIIDLDGNIQDDPVVRGNRPDFT
MQPGVDINGNSDGTVDILKGMNRLSEKMIMALKNEYSRTNLQNKSNITNDEEDEDNDERN
ELKIDDLNESYKTNYAIIHLKRNAHEKTTDNDAKSSADSIKNADLKVSNQQMLQQLSLVM
DNLINKLDLNQVVPNNEVSNKINKRVITAIKINAKQAKHNNVNSALGSFVDNTSQANELE
VKSTLPIDLLESCRMLHTTCCEFLKHFYIHFQSGEQKQASTVKKLYNHLKDCIEKLNELF
QDVLNGDGESMSNTCTAYLKPVLNSITLATHKYDEYFNEYNNNSN
Sequence of entity 3 (2), FASTA
>7O4I_3 General transcription and DNA repair factor IIH subunit TFB2 (chains 2)
GPGSMSDYSLKHSVTQYLEEIPQQVQNRLYTSPATCLAIYRILPPLAKFFIMAMVFNENE
VPLLDLDKWVNSNGKLQFQNAIKSMKSLHLLIPNKSSGTLMINLNPTFKISLRNALTGGE
VQNSFGVVVEENVVSLDLLDEYSANKWETILHFMVGTPLAKIPSEKVLNLLKHSKLMEEV
NSTGEFKITNEGFQFLLQEINSQLWTLLLQYLKMIETSKMDLVDVLHFIFMLGALEVGKA
YKIDALSETQRIMLQDMRDYGLVFQKHSNDSIFYPTKLALMLTSDTKTIRSASNAMDSVL
RQNREEPSVNEDGANGKSTTDITTSDDLNKAGLKNQDIPDGSLIVETNFKIYSYSNSPLQ
IAVLSLFVHLKARFVNMVLGQITRESIRRALTNGITADQIIAYLETHAHPQMRRLAEEKL
EKKLELDPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQ
DIGVLLWKDDKKKKFFISKEGNSQVLDFAKRKLKKKQ
Sequence of entity 4 (3), FASTA
>7O4I_4 RNA polymerase II transcription factor B subunit 3 (chains 3)
GPHMLMDEYEENKDMCPICKTDRYLSPDVKFLVNPECYHRICESCVDRIFSLGPAQCPYK
GCDKILRKNKFKTQIFDDVEVEKEVDIRKRVFNVFNKTIDDFNGDLVEYNKYLEEVEDII
YKLDHGIDVAKTEEKLRTYEELNKQLIMNNLERSRTEIESFEQRQKFEKEMKLKKRLLER
QIEEEERMNKEWTKKEIVNRLSTTTQDINETIEGVKNTVKLKKSSARRKLEELNRVLKNN
PYFNSNVNVQNSRLKDAVPFTPFNGDREAHPRFTLKGSVYNDPFIKDLEHRKEFIASGFN
TNYAYERVLTEAFMGLGCVISEEL
Sequence of entity 5 (4), FASTA
>7O4I_5 General transcription and DNA repair factor IIH subunit TFB4 (chains 4)
SNAMDAISDPTFKHARSRKQVTEESPSLLTVIIEIAPKLWTTFDEEGNEKGSIIKVLEAL
IVFLNAHLAFNSANKVAVIAAYSQGIKYLYPESTSALKASESENKTRSDLKIINSDMYRR
FRNVDETLVEEIYKLFELEKKQIEQNSQRSTLAGAMSAGLTYVNRISKESVTTSLKSRLL
VLTCGSGSSKDEIFQYIPIMNCIFSATKMKCPIDVVKIGGSKESTFLQQTTDATNGVYLH
VESTEGLIQYLATAMFIDPSLRPIIVKPNHGSVDFRTSCYLTGRVVAVGFICSVCLCVLS
IIPPGNKCPACDSQFDEHVIAKLKRKPVVPRLKAKKKVTKP
Sequence of entity 6 (5), FASTA
>7O4I_6 General transcription and DNA repair factor IIH subunit TFB5 (chains 5)
GPGSMARARKGALVQCDPSIKALILQIDAKMSDIVLEELDDTHLLVNPSKVEFVKHELNR
LLSKNIYNPMDEEENQ
Sequence of entity 7 (6), FASTA
>7O4I_7 General transcription and DNA repair factor IIH subunit SSL1 (chains 6)
GGSMAPVVISESEEDEDRVAITRRTKRQVHFDGEGDDRVDQQQQQHSSSHRDRDKHVQRK
KKKRLSNRNLQGSNGGYAWEDEIKRSWDLVKVDDEGDMASLVASIVEARKKRTAKKNITP
YQRGIIRSLILTLDCSEAMLEKDLRPNRHAMIIQYAIDFVHEFFDQNPISQMGIIIMRNG
LAQLVSQVSGNPQDHIDALKSIRKQEPKGNPSLQNALEMARGLLLPVPAHCTREVLIVFG
SLSTTDPGDIHQTIDSLVSEKIRVKVLGLSAQVAICKELCKATNYGDESFYKILLDETHL
KELFNEAVTPLPVNKINKGFTLVKMGFPTRIFEDTPTFCSCHSKLVYGGYFCPNCHSKVC
SLPTVCPCCDLMLILSTHLARSYHHLMPLKTFAEVPTTEKFRSEDCFSCQSRFPILKNHK
NGKLLTSSRYRCEDCKQEFCVDCDVFIHEILHNCPGCESKPVIT
Sequence of entity 8 (7), FASTA
>7O4I_8 General transcription and DNA repair factor IIH helicase subunit XPB (chains 7)
MTDVEGYQPKSKGKIFPDMGESFFSSDEDSPATDAEIDENYDDNRETSEGRGERDTGAMV
TGLKKPRKKTKSSRHTAADSSMNQMDAKDKALLQDTNSDIPADFVPDSVSGMFRSHDFSY
LRLRPDHASRPLWISPSDGRIILESFSPLAEQAQDFLVTIAEPISRPSHIHEYKITAYSL
YAAVSVGLETDDIISVLDRLSKVPVAESIINFIKGATISYGKVKLVIKHNRYFVETTQAD
ILQMLLNDSVIGPLRIDSDHQVQPPEDVLQQQLQQTAGKPATNVNPNDVEAVFSAVIGGD
NEREEEDDDIDAVHSFEIANESVEVVKKRCQEIDYPVLEEYDFRNDHRNPDLDIDLKPST
QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGITAACTIKKSVIVLCTSSVSVMQW
RQQFLQWCTLQPENCAVFTSDNKEMFQTESGLVVSTYSMVANTRNRSHDSQKVMDFLTGR
EWGFIILDEVHVVPAAMFRRVVSTIAAHAKLGLTATLVREDDKIGDLNFLIGPKLYEANW
MELSQKGHIANVQCAEVWCPMTAEFYQEYLRETARKRMLLYIMNPTKFQACQFLIQYHER
RGDKIIVFSDNVYALQEYALKMGKPFIYGSTPQQERMNILQNFQYNDQINTIFLSKVGDT
SIDLPEATCLIQISSHYGSRRQEAQRLGRILRAKRRNDEGFNAFFYSLVSKDTQEMYYST
KRQAFLVDQGYAFKVITHLHGMENIPNLAYASPRERRELLQEVLLKNEEAAGIEVGDDAD
NSVGRGSNGHKRFKSKAVRGEGSLSGLAGGEDMAYMEYSTNKNKELKEHHPLIRKMYYKN
LKK
Sequence of entity 9 (A), FASTA
>7O4I_9 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
Sequence of entity 10 (B), FASTA
>7O4I_10 DNA-directed RNA polymerase II subunit RPB2 (chains B)
MSDLANSEKYYDEDPYGFEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQ
DIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLR
NLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCY
LSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEI
RSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEH
ICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEF
LPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTL
FKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVS
QVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLS
LMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETL
RTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAK
LMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEEND
LDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGV
FLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMI
MNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIA
PGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDG
LKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSR
MTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKK
LMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIA
HGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAA
KLLFQELMAMNITPRLYTDRSRDF
Sequence of entity 11 (C), FASTA
>7O4I_11 DNA-directed RNA polymerase II subunit RPB3 (chains C)
MGSHHHHHHSNSGLNDIFEAQKIEWHEDTGSSEGPQVKIREASKDNVDFILSNVDLAMAN
SLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEYSRDCFCEDH
CDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQ
ELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYED
PPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQDKVN
FASGDNNTASNMLGSNEDVMMTGAEQDPYSNASQMGNTGSGGYDNAW
Sequence of entity 12 (D), FASTA
>7O4I_12 DNA-directed RNA polymerase II subunit RPB4 (chains D)
MNVSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIK
EALVERRRAFKRSQKKHKKKHLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETRE
KELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQL
GSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 1 |
| MG | Magnesium ion | Mg | 2 |
| BEF | Beryllium trifluoride ion | Be F3 | 1 |
| ZN | Zinc ion | Zn | 17 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 1 |
Primary citation
Structure of RNA polymerase II pre-initiation complex at 2.9 angstrom defines initial DNA opening. Schilbach, S., Aibara, S., Dienemann, C. et al. Cell (2021) 184:4064-4072.e28. DOI 10.1016/j.cell.2021.05.012 · PubMed
Other PDB entries of the same protein (UniProt P06839 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7O4J 2.9 Å, Yeast RNA polymerase II transcription pre-initiation complex (consensus)
- 7ML0 3.0 Å, RNA polymerase II pre-initiation complex (PIC1)
- 8CEN 3.0 Å, Yeast RNA polymerase II transcription pre-initiation complex with core Mediator
- 7ML4 3.1 Å, RNA polymerase II initially transcribing complex (ITC)
- 7ZS9 3.1 Å, Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome…
- 7O75 3.2 Å, Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA
- 7ML2 3.4 Å, RNA polymerase II pre-initiation complex (PIC3)
- 7O4L 3.4 Å, Yeast TFIIH in the expanded state within the pre-initiation complex
- 7O72 3.4 Å, Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA
- 7O73 3.4 Å, Yeast RNA polymerase II transcription pre-initiation complex with closed distorted…
- 7O4K 3.6 Å, Yeast TFIIH in the contracted state within the pre-initiation complex
- 8CEO 3.6 Å, Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the…
Browse structure collections
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