7AD8: PDB entry 7AD8
Core TFIIH-XPA-DNA complex with modelled p62 subunit. Determined by electron microscopy at 3.5 Å resolution. Released 28 Jul 2021.
- Method
- Electron microscopy
- Resolution
- 3.5 Å
- Organism
- Homo sapiens
- Chains
- 10
- Atoms
- 21,213
- Mol. weight
- 440.02 kDa
- Ligands
- SF4, ZN
- Released
- 28 Jul 2021
Explore 7AD8 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7AD8 contains 129 α-helices and 93 β-strands across 8 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: 29 helices, 32 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 78 | 1 | 1 |
| β-strand | 84-87 | 4 | 1 |
| α-helix | 94-100 | 7 | |
| β-strand | 105-108 | 4 | 1 |
| β-strand | 113-117 | 5 | 1 |
| α-helix | 120-128 | 9 | |
| α-helix | 133-139 | 7 | |
| α-helix | 153-158 | 6 | |
| β-strand | 166-170 | 5 | 2 |
| β-strand | 175-179 | 5 | 2 |
| α-helix | 182-188 | 7 | |
| α-helix | 194-196 | 3 | |
| β-strand | 198 | 1 | 3 |
| β-strand | 268-271 | 4 | 2 |
| β-strand | 272 | 1 | 3 |
| α-helix | 277-286 | 10 | |
| α-helix | 290-291 | 2 | |
| β-strand | 292 | 1 | 2 |
| β-strand | 295 | 1 | 4 |
| α-helix | 320-327 | 8 | |
| β-strand | 333 | 1 | 4 |
| β-strand | 337-339 | 3 | 5 |
| α-helix | 348-357 | 10 | |
| β-strand | 361-365 | 5 | 5 |
| α-helix | 370-381 | 12 | |
| β-strand | 389-391 | 3 | 5 |
| β-strand | 405-409 | 5 | 5 |
| α-helix | 418-420 | 3 | |
| α-helix | 421-430 | 10 | |
| β-strand | 435 | 1 | 6 |
| β-strand | 438-441 | 4 | 5 |
| α-helix | 443-445 | 3 | |
| α-helix | 454-457 | 4 | |
| β-strand | 460 | 1 | 6 |
| β-strand | 463-467 | 5 | 5 |
| α-helix | 473-475 | 3 | |
| α-helix | 480-483 | 4 | |
| β-strand | 487-490 | 4 | 5 |
| α-helix | 493-498 | 6 | |
| β-strand | 505 | 1 | 7 |
| β-strand | 508-510 | 3 | 8 |
| β-strand | 511-512 | 2 | 9 |
| α-helix | 513-515 | 3 | |
| α-helix | 519-522 | 4 | |
| α-helix | 530-535 | 6 | |
| α-helix | 538-552 | 15 | |
| β-strand | 558-559 | 2 | 10 |
| α-helix | 566-572 | 7 | |
| β-strand | 579-580 | 2 | 11 |
| α-helix | 587-595 | 9 | |
| β-strand | 606-607 | 2 | 11 |
| β-strand | 622-626 | 5 | 10 |
| α-helix | 635-637 | 3 | |
| α-helix | 640-642 | 3 | |
| β-strand | 657 | 1 | 7 |
| β-strand | 658-662 | 5 | 10 |
| β-strand | 663-664 | 2 | 9 |
| α-helix | 669-676 | 8 | |
| α-helix | 680-683 | 4 | |
| β-strand | 688-690 | 3 | 8 |
| α-helix | 707-716 | 10 | |
Chain B: 28 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-3 | 2 | 14 |
| β-strand | 10-11 | 2 | 14 |
| α-helix | 19-32 | 14 | |
| β-strand | 38-41 | 4 | 15 |
| α-helix | 48-62 | 15 | |
| β-strand | 69-73 | 5 | 15 |
| α-helix | 77-98 | 22 | |
| β-strand | 106-108 | 3 | 15 |
| α-helix | 127-138 | 12 | |
| α-helix | 145-147 | 3 | |
| α-helix | 156-164 | 9 | |
| α-helix | 177-187 | 11 | |
| α-helix | 191-197 | 7 | |
| β-strand | 204-207 | 4 | 15 |
| α-helix | 215-221 | 7 | |
| β-strand | 229-234 | 6 | 15 |
| α-helix | 239-245 | 7 | |
| β-strand | 249-252 | 4 | 16 |
| α-helix | 253-270 | 18 | |
| α-helix | 327-344 | 18 | |
| β-strand | 351-352 | 2 | 16 |
| α-helix | 357-360 | 4 | |
| α-helix | 375-386 | 12 | |
| α-helix | 395-404 | 10 | |
| β-strand | 414-419 | 6 | 16 |
| β-strand | 432-437 | 6 | 16 |
| α-helix | 447-450 | 4 | |
| β-strand | 453-458 | 6 | 15 |
| α-helix | 467-470 | 4 | |
| β-strand | 490-493 | 4 | 17 |
| β-strand | 495 | 1 | 18 |
| α-helix | 514-527 | 14 | |
| β-strand | 535-539 | 5 | 17 |
| α-helix | 542-553 | 12 | |
| α-helix | 558-564 | 7 | |
| β-strand | 566-569 | 4 | 17 |
| α-helix | 574-587 | 14 | |
| β-strand | 594-599 | 6 | 17 |
| α-helix | 603-607 | 5 | |
| β-strand | 617-620 | 4 | 17 |
| α-helix | 633-642 | 10 | |
| α-helix | 648-656 | 9 | |
| α-helix | 665-667 | 3 | |
| β-strand | 675-679 | 5 | 17 |
| α-helix | 682-685 | 4 | |
| α-helix | 687-690 | 4 | |
| β-strand | 708 | 1 | 18 |
| α-helix | 710-724 | 15 | |
Chain C: 27 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-24 | 6 | |
| α-helix | 28-34 | 7 | |
| α-helix | 40-46 | 7 | |
| α-helix | 52-58 | 7 | |
| α-helix | 65-67 | 3 | |
| β-strand | 75 | 1 | 20 |
| α-helix | 81-92 | 12 | |
| β-strand | 96 | 1 | 26 |
| α-helix | 109 | 1 | |
| β-strand | 110 | 1 | 26 |
| α-helix | 111 | 1 | |
| α-helix | 112-121 | 10 | |
| α-helix | 147-160 | 14 | |
| α-helix | 161-163 | 3 | |
| α-helix | 173-182 | 10 | |
| α-helix | 198-204 | 7 | |
| α-helix | 210-226 | 17 | |
| α-helix | 230-240 | 11 | |
| α-helix | 257-268 | 12 | |
| α-helix | 285-288 | 4 | |
| β-strand | 314-317 | 4 | 27 |
| α-helix | 322-328 | 7 | |
| β-strand | 333-338 | 6 | 27 |
| β-strand | 341-345 | 5 | 27 |
| α-helix | 348-355 | 8 | |
| α-helix | 362-370 | 9 | |
| α-helix | 381 | 1 | |
| α-helix | 385-399 | 15 | |
| β-strand | 402-404 | 3 | 13 |
| β-strand | 407-409 | 3 | 12 |
| α-helix | 417-420 | 4 | |
| α-helix | 421-424 | 4 | |
| α-helix | 426-428 | 3 | |
| β-strand | 431 | 1 | 12 |
| β-strand | 441-443 | 3 | 12 |
| α-helix | 445-447 | 3 | |
| α-helix | 451-456 | 6 | |
Chain D: 14 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 59-66 | 8 | 24 |
| α-helix | 69-72 | 4 | |
| α-helix | 80-95 | 16 | |
| β-strand | 103-109 | 7 | 24 |
| β-strand | 114-121 | 8 | 24 |
| α-helix | 128-131 | 4 | |
| α-helix | 133-136 | 4 | |
| α-helix | 148-154 | 7 | |
| β-strand | 164-171 | 8 | 24 |
| α-helix | 185-191 | 7 | |
| β-strand | 195-200 | 6 | 24 |
| α-helix | 207-215 | 9 | |
| β-strand | 219-221 | 3 | 24 |
| α-helix | 225-232 | 8 | |
| α-helix | 238-239 | 2 | |
| β-strand | 279-280 | 2 | 23 |
| β-strand | 282 | 1 | 25 |
| β-strand | 283 | 1 | 22 |
| α-helix | 303-305 | 3 | |
| β-strand | 311 | 1 | 25 |
| α-helix | 315-319 | 5 | |
| α-helix | 327-330 | 4 | |
| α-helix | 369-374 | 6 | |
| α-helix | 375-379 | 5 | |
Chain E: 12 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10-15 | 6 | 19 |
| α-helix | 19-28 | 10 | |
| α-helix | 35-48 | 14 | |
| β-strand | 56-62 | 7 | 19 |
| β-strand | 67-69 | 3 | 19 |
| α-helix | 109-118 | 10 | |
| α-helix | 134-147 | 14 | |
| β-strand | 159-165 | 7 | 19 |
| α-helix | 171-173 | 3 | |
| α-helix | 174-177 | 4 | |
| α-helix | 179-185 | 7 | |
| β-strand | 190-195 | 6 | 19 |
| α-helix | 201-209 | 9 | |
| β-strand | 214-216 | 3 | 19 |
| α-helix | 223-226 | 4 | |
| α-helix | 227-231 | 5 | |
| α-helix | 235-238 | 4 | |
| β-strand | 241 | 1 | 20 |
| α-helix | 244-246 | 3 | |
| β-strand | 253-254 | 2 | 21 |
| β-strand | 261-262 | 2 | 21 |
| β-strand | 264 | 1 | 22 |
| β-strand | 266-268 | 3 | 23 |
| β-strand | 274-275 | 2 | 23 |
Chain F: 2 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6 | 1 | 12 |
| β-strand | 8-11 | 4 | 13 |
| α-helix | 14-22 | 9 | |
| β-strand | 34-37 | 4 | 13 |
| β-strand | 42-45 | 4 | 13 |
| α-helix | 50-61 | 12 | |
Chain G: 6 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 138-140 | 3 | 28 |
| α-helix | 143-146 | 4 | |
| α-helix | 161-162 | 2 | |
| β-strand | 165 | 1 | 28 |
| β-strand | 168 | 1 | 29 |
| β-strand | 177 | 1 | 29 |
| β-strand | 180-182 | 3 | 28 |
| α-helix | 183-193 | 11 | |
| α-helix | 197-199 | 3 | |
| α-helix | 200-226 | 27 | |
| α-helix | 228-235 | 8 | |
Chain I: 11 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 297-301 | 5 | |
| α-helix | 313-321 | 9 | |
| α-helix | 325-327 | 3 | |
| α-helix | 333-342 | 10 | |
| α-helix | 400-410 | 11 | |
| α-helix | 424-433 | 10 | |
| α-helix | 441-444 | 4 | |
| α-helix | 457-478 | 22 | |
| α-helix | 486-504 | 19 | |
| α-helix | 509-513 | 5 | |
| α-helix | 523-546 | 24 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| DNA (49-mer) | J | DNA | 49 | Homo sapiens | |
| DNA (49-mer) | K | DNA | 49 | Homo sapiens | |
| General transcription and DNA repair factor IIH helicase subunit XPB | A | protein | 782 | Homo sapiens | P19447 (AlphaFold model) |
| General transcription factor IIH subunit 5 | F | protein | 71 | Homo sapiens | Q6ZYL4 (AlphaFold model) |
| TFIIH basal transcription factor complex helicase XPD subunit | B | protein | 760 | Homo sapiens | P18074 (AlphaFold model) |
| General transcription factor IIH subunit 3 | E | protein | 308 | Homo sapiens | Q13889 (AlphaFold model) |
| General transcription factor IIH subunit 2 | D | protein | 395 | Homo sapiens | Q13888 |
| General transcription factor IIH subunit 4 | C | protein | 462 | Homo sapiens | Q92759 |
| DNA repair protein complementing XP-A cells | G | protein | 273 | Homo sapiens | P23025 |
| General transcription factor IIH subunit 1 | I | protein | 548 | Homo sapiens | P32780 |
Sequence of entity 1 (J), FASTA
>7AD8_1 DNA (49-MER) (chains J)
CAAAGTCACGACCTAGACACTGCGAGCTCGAATTCACTGGAGTGACCTC
Sequence of entity 2 (K), FASTA
>7AD8_2 DNA (49-MER) (chains K)
GAGGTCACTCCAGTGAATTCGAGCTCGCAACAATGAGCACATACCTAGT
Sequence of entity 3 (A), FASTA
>7AD8_3 General transcription and DNA repair factor IIH helicase subunit XPB (chains A)
MGKRDRADRDKKKSRKRHYEDEEDDEEDAPGNDPQEAVPSAAGKQVDESGTKVDEYGAKD
YRLQMPLKDDHTSRPLWVAPDGHIFLEAFSPVYKYAQDFLVAIAEPVCRPTHVHEYKLTA
YSLYAAVSVGLQTSDITEYLRKLSKTGVPDGIMQFIKLCTVSYGKVKLVLKHNRYFVESC
HPDVIQHLLQDPVIRECRLRNSEGEATELITETFTSKSAISKTAESSGGPSTSRVTDPQG
KSDIPMDLFDFYEQMDKDEEEEEETQTVSFEVKQEMIEELQKRCIHLEYPLLAEYDFRND
SVNPDINIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKR
CLVLGNSAVSVEQWKAQFKMWSTIDDSQICRFTSDAKDKPIGCSVAISTYSMLGHTTKRS
WEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLTATLVREDDKIVDL
NFLIGPKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNK
FRACQFLIKFHERRNDKIIVFADNVFALKEYAIRLNKPYIYGPTSQGERMQILQNFKHNP
KINTIFISKVGDTSFDLPEANVLIQISSHGGSRRQEAQRLGRVLRAKKGMVAEEYNAFFY
SLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEEDLAFSTKEEQQQLLQKVLAAT
DLDAEEEVVAGEFGSRSSQASRRFGTMSSMSGADDTVYMEYHSSRSKAPSKHVHPLFKRF
RK
Sequence of entity 4 (F), FASTA
>7AD8_4 General transcription factor IIH subunit 5 (chains F)
MVNVLKGVLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGEL
MDQNAFSLTQK
Sequence of entity 5 (B), FASTA
>7AD8_5 TFIIH basal transcription factor complex helicase XPD subunit (chains B)
MKLNVDGLLVYFPYDYIYPEQFSYMRELKRTLDAKGHGVLEMPSGTGKTVSLLALIMAYQ
RAYPLEVTKLIYCSRTVPEIEKVIEELRKLLNFYEKQEGEKLPFLGLALSSRKNLCIHPE
VTPLRFGKDVDGKCHSLTASYVRAQYQHDTSLPHCRFYEEFDAHGREVPLPAGIYNLDDL
KALGRRQGWCPYFLARYSILHANVVVYSYHYLLDPKIADLVSKELARKAVVVFDEAHNID
NVCIDSMSVNLTRRTLDRCQGNLETLQKTVLRIKETDEQRLRDEYRRLVEGLREASAARE
TDAHLANPVLPDEVLQEAVPGSIRTAEHFLGFLRRLLEYVKWRLRVQHVVQESPPAFLSG
LAQRVCIQRKPLRFCAERLRSLLHTLEITDLADFSPLTLLANFATLVSTYAKGFTIIIEP
FDDRTPTIANPILHFSCMDASLAIKPVFERFQSVIITSGTLSPLDIYPKILDFHPVTMAT
FTMTLARVCLCPMIIGRGNDQVAISSKFETREDIAVIRNYGNLLLEMSAVVPDGIVAFFT
SYQYMESTVASWYEQGILENIQRNKLLFIETQDGAETSVALEKYQEACENGRGAILLSVA
RGKVSEGIDFVHHYGRAVIMFGVPYVYTQSRILKARLEYLRDQFQIRENDFLTFDAMRHA
AQCVGRAIRGKTDYGLMVFADKRFARGDKRGKLPRWIQEHLTDANLNLTVDEGVQVAKYF
LRQMAQPFHREDQLGLSLLSLEQLESEETLKRIEQIAQQL
Sequence of entity 6 (E), FASTA
>7AD8_6 General transcription factor IIH subunit 3 (chains E)
MVSDEDELNLLVIVVDANPIWWGKQALKESQFTLSKCIDAVMVLGNSHLFMNRSNKLAVI
ASHIQESRFLYPGKNGRLGDFFGDPGNPPEFNPSGSKDGKYELLTSANEVIVEEIKDLMT
KSDIKGQHTETLLAGSLAKALCYIHRMNKEVKDNQEMKSRILVIKAAEDSALQYMNFMNV
IFAAQKQNILIDACVLDSDSGLLQQACDITGGLYLKVPQMPSLLQYLLWVFLPDQDQRSQ
LILPPPVHVDYRAACFCHRNLIEIGYVCSVCLSIFCNFSPICTTCETAFKISLPPVLKAK
KKKLKVSA
Sequence of entity 7 (D), FASTA
>7AD8_7 General transcription factor IIH subunit 2 (chains D)
MDEEPERTKRWEGGYERTWEILKEDESGSLKATIEDILFKAKRKRVFEHHGQVRLGMMRH
LYVVVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTEL
SGNPRKHITSLKKAVDMTCHGEPSLYNSLSIAMQTLKHMPGHTSREVLIIFSSLTTCDPS
NIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETGGTYHVILDESHYKELLTHHVSPPP
ASSSSECSLIRMGFPQHTIASLSDQDAKPSFSMAHLDGNTEPGLTLGGYFCPQCRAKYCE
LPVECKICGLTLVSAPHLARSYHHLFPLDAFQEIPLEEYNGERFCYGCQGELKDQHVYVC
AVCQNVFCVDCDVFVHDSLHCCPGCIHKIPAPSGV
Sequence of entity 8 (C), FASTA
>7AD8_8 General transcription factor IIH subunit 4 (chains C)
MESTPSRGLNRVHLQCRNLQEFLGGLSPGVLDRLYGHPATCLAVFRELPSLAKNWVMRML
FLEQPLPQAAVALWVKKEFSKAQEESTGLLSGLRIWHTQLLPGGLQGLILNPIFRQNLRI
ALLGGGKAWSDDTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQLLS
QAGLMKSTEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQL
SFSTLGKDYSVEGMSDSLLNFLQHLREFGLVFQRKRKSRRYYPTRLAINLSSGVSGAGGT
VHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGIT
AQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFEL
LLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQKHSS
Sequence of entity 9 (G), FASTA
>7AD8_9 DNA repair protein complementing XP-A cells (chains G)
MAAADGALPEAAALEQPAELPASVRASIERKRQRALMLRQARLAARPYSATAAAATGGMA
NVKAAPKIIDTGGGFILEEEEEEEQKIGKVVHQPGPVMEFDYVICEECGKEFMDSYLMNH
FDLPTCDNCRDADDKHKLITKTEAKQEYLLKDCDLEKREPPLKFIVKKNPHHSQWGDMKL
YLKLQIVKRSLEVWGSQEALEEAKEVRQENREKMKQKKFDKKVKELRRAVRSSVWKRETI
VHQHEYGPEENLEDDMYRKTCTMCGHELTYEKM
Sequence of entity 10 (I), FASTA
>7AD8_10 General transcription factor IIH subunit 1 (chains I)
MATSSEEVLLIVKKVRQKKQDGALYLMAERIAWAPEGKDRFTISHMYADIKCQKISPEGK
AKIQLQLVLHAGDTTNFHFSNESTAVKERDAVKDLLQQLLPKFKRKANKELEEKNRMLQE
DPVLFQLYKDLVVSQVISAEEFWANRLNVNATDSSSTSNHKQDVGISAAFLADVRPQTDG
CNGLRYNLTSDIIESIFRTYPAVKMKYAENVPHNMTEKEFWTRFFQSHYFHRDRLNTGSK
DLFAECAKIDEKGLKTMVSLGVKNPLLDLTALEDKPLDEGYGISSVPSASNSKSIKENSN
AAIIKRFNHHSAMVLAAGLRKQEAQNEQTSEPSNMDGNSGDADCFQPAVKRAKLQESIEY
EDLGKNNSVKTIALNLKKSDRYYHGPTPIQSLQYATSQDIINSFQSIRQEMEAYTPKLTQ
VLSSSAASSTITALSPGGALMQGGTQQAINQMVPNDIQSELKHLYVAVGELLRHFWSCFP
VNTPFLEEKVVKMKSNLERFQVTKLCPFQEKIRRQYLSTNLVSHIEEMLQTAYNKLHTWQ
SRRLMKKT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| SF4 | Iron/sulfur cluster | Fe4 S4 | 1 |
| ZN | Zinc ion | Zn | 6 |
Primary citation
The TFIIH subunits p44/p62 act as a damage sensor during nucleotide excision repair. Barnett, J.T., Kuper, J., Koelmel, W. et al. Nucleic Acids Res (2020) 48:12689-12696. DOI 10.1093/nar/gkaa973 · PubMed
Other PDB entries of the same protein (UniProt P19447 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4ERN 1.8 Å, Crystal structure of the C-terminal domain of human XPB/ERCC-3 excision repair protein…
- 7NVV 2.9 Å, XPB-containing part of TFIIH in a post-translocated state (with ADP-BeF3)
- 28JM 3.29 Å, Cryo-EM structure of the human holo-TFIIH and XPC initial encounter complex
- 7EGB 3.3 Å, TFIID-based holo PIC on SCP promoter
- 8EBU 3.3 Å, XPC release from Core7-XPA-DNA (Cy5)
- 9PD3 3.3 Å, NER dual incision complex - DuIS
- 28JS 3.32 Å, Cryo-EM structure of the human holo-TFIIH-XPC complex bound to bulky lesion-mimic DNA…
- 9PD4 3.4 Å, NER dual incision complex - DuIM
- 6RO4 3.5 Å, Structure of the core TFIIH-XPA-DNA complex
- 9XYU 3.5 Å, NER complex - C7CAD.ATP
- 28KE 3.6 Å, Cryo-EM structure of the human holo-TFIIH-XPC-XPA complex bound to bulky lesion-mimic DNA
- 8EBX 3.6 Å, XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (AP)
Browse structure collections
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