7K01: PDB entry 7K01

Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex. Determined by electron microscopy at 3.9 Å resolution. Released 28 Jul 2021.

Method: Electron microscopy
Resolution: 3.9 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 7
Atoms: 21,052
Mol. weight: 415.75 kDa
Ligands: SF4, ZN
Released: 28 Jul 2021

Explore 7K01 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7K01 contains 136 α-helices and 110 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 0: 39 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	26
β-strand	9-10	2	26
α-helix	19-33	15
β-strand	40-41	2	27
α-helix	48-62	15
β-strand	69-71	3	27
α-helix	76-97	22
β-strand	105-108	4	27
α-helix	118-122	5
α-helix	126-136	11
α-helix	141-147	7
α-helix	158-161	4
α-helix	162-166	5
α-helix	178-187	10
α-helix	192-199	8
β-strand	205-208	4	27
α-helix	211-214	4
β-strand	231-235	5	27
α-helix	241-248	8
β-strand	250	1	28
β-strand	253	1	29
α-helix	254-277	24
α-helix	280-291	12
α-helix	295-298	4
α-helix	323-326	4
α-helix	328-346	19
β-strand	352	1	30
α-helix	356-366	11
α-helix	371-375	5
α-helix	377-388	12
α-helix	394-396	3
α-helix	397-411	15
β-strand	416-418	3	28
β-strand	420	1	30
β-strand	421	1	29
α-helix	425-427	3
β-strand	434	1	29
β-strand	437-439	3	28
α-helix	443-452	10
β-strand	456-460	5	27
α-helix	468-473	6
β-strand	481-482	2	27
β-strand	494	1	31
β-strand	499	1	32
β-strand	505	1	32
α-helix	516-532	17
β-strand	537-541	5	33
α-helix	544-556	13
α-helix	559-566	8
β-strand	568-571	4	33
α-helix	576-591	16
β-strand	596-601	6	33
α-helix	605-609	5
β-strand	619	1	33
β-strand	620	1	31
β-strand	623	1	34
α-helix	634-645	12
α-helix	650-666	17
α-helix	667-669	3
β-strand	679	1	31
β-strand	682	1	34
α-helix	686-689	4
α-helix	695-700	6
α-helix	703-705	3
β-strand	709	1	32
α-helix	710-725	16
α-helix	734-737	4
α-helix	744-751	8

Chain 1: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	171-176	6
α-helix	178-187	10
α-helix	189-197	9
α-helix	206-224	19
α-helix	227-229	3
α-helix	231-236	6
α-helix	252-262	11
α-helix	264-272	9
α-helix	282-294	13
α-helix	310-329	20
α-helix	339-342	4
α-helix	372-390	19
α-helix	468-482	15
α-helix	497-515	19
α-helix	541-564	24
α-helix	576-604	29
α-helix	607-638	32

Chain 2: 23 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	10-16	7
α-helix	19-26	8
α-helix	29-36	8
α-helix	41-50	10
β-strand	57-58	2	22
α-helix	59-64	6
β-strand	66	1	4
α-helix	71-84	14
β-strand	87	1	23
β-strand	97-98	2	22
β-strand	100	1	23
α-helix	102-112	11
α-helix	120-122	3
β-strand	124	1	24
α-helix	136-151	16
α-helix	161-169	9
α-helix	186-193	8
α-helix	197-210	14
α-helix	218-230	13
β-strand	234	1	24
α-helix	244-255	12
α-helix	273-279	7
α-helix	354-361	8
β-strand	369	1	25
β-strand	374	1	25
α-helix	380-388	9
α-helix	395-402	8
α-helix	405-407	3
α-helix	409-416	8
α-helix	435-447	13
β-strand	452-453	2	21
β-strand	457-458	2	20
α-helix	465-478	14
β-strand	492-493	2	20
α-helix	496-506	11

Chain 4: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	26-29	4	1
β-strand	30	1	2
α-helix	34-42	9
α-helix	51-67	17
β-strand	73-76	4	1
β-strand	79	1	3
β-strand	82	1	3
β-strand	85	1	1
α-helix	117-134	18
α-helix	138-142	5
α-helix	149-166	18
β-strand	175-176	2	1
β-strand	179-182	4	2
α-helix	193-206	14
β-strand	210	1	1
β-strand	212-216	5	2
α-helix	222-230	9
β-strand	235-238	4	2
α-helix	245-251	7
β-strand	261	1	4
β-strand	275	1	5
β-strand	282	1	5
α-helix	283	1
β-strand	287-288	2	6
β-strand	295-296	2	6
α-helix	314-321	8

Chain 5: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	20
β-strand	8-11	4	21
α-helix	14-26	13
β-strand	33-36	4	21
β-strand	39-42	4	21
α-helix	44-61	18

Chain 6: 13 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	125-129	5	35
α-helix	134-137	4
α-helix	145-163	19
β-strand	168-172	5	35
β-strand	175	1	36
β-strand	178	1	36
β-strand	181-186	6	35
α-helix	189-200	12
α-helix	210-220	11
β-strand	230-234	5	35
α-helix	247-256	10
β-strand	261-263	3	35
α-helix	271-280	10
α-helix	294-305	12
β-strand	320-321	2	6
β-strand	322-323	2	37
β-strand	347-348	2	38
β-strand	355-356	2	38
β-strand	362	1	37
β-strand	369-370	2	37
α-helix	374-383	10
α-helix	386-389	4
β-strand	390	1	39
α-helix	391-393	3
α-helix	419-422	4
β-strand	428	1	39
α-helix	438-446	9
α-helix	452-455	4

Chain 7: 32 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	105-108	4
α-helix	122-124	3
α-helix	125-127	3
β-strand	132	1	7
β-strand	133	1	8
β-strand	142	1	8
α-helix	150-160	11
β-strand	162	1	9
β-strand	174	1	9
α-helix	177-186	10
α-helix	190-200	11
β-strand	201	1	7
α-helix	204-206	3
α-helix	207-218	12
β-strand	223	1	10
β-strand	233	1	11
α-helix	239-247	9
β-strand	255	1	12
α-helix	263-267	5
β-strand	317	1	11
β-strand	318	1	12
α-helix	323-332	10
β-strand	337	1	10
β-strand	341	1	13
α-helix	350-352	3
β-strand	353	1	14
α-helix	364-374	11
β-strand	379	1	13
β-strand	382-385	4	15
α-helix	392-403	12
β-strand	407-411	5	16
α-helix	414-420	7
α-helix	421-425	5
β-strand	437	1	16
β-strand	451	1	14
β-strand	453-456	4	16
α-helix	457-460	4
α-helix	469-479	11
β-strand	484-486	3	16
β-strand	488	1	15
α-helix	495-505	11
β-strand	511-514	4	15
α-helix	527-531	5
β-strand	534	1	15
α-helix	540-546	7
β-strand	552-555	4	17
β-strand	558-559	2	18
α-helix	560-561	2
α-helix	563-571	9
α-helix	577-582	6
α-helix	585-601	17
β-strand	605-608	4	17
α-helix	613-622	10
α-helix	633-644	12
β-strand	651-654	4	17
α-helix	663-665	3
β-strand	666	1	19
α-helix	667	1
β-strand	669-672	4	17
α-helix	682-690	9
β-strand	692	1	19
β-strand	703-707	5	17
β-strand	709-710	2	18
α-helix	716-729	14
β-strand	732-734	3	17
α-helix	753-765	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
General transcription and DNA repair factor IIH subunit TFB1	1	protein	642	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32776 (AlphaFold model)
General transcription and DNA repair factor IIH subunit TFB4	4	protein	338	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q12004 (AlphaFold model)
DNA repair helicase RAD25	7	protein	843	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q00578 (AlphaFold model)
RNA polymerase II transcription factor B subunit 5	5	protein	72	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q3E7C1 (AlphaFold model)
General transcription and DNA repair factor IIH subunit TFB2	2	protein	513	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q02939
DNA repair helicase RAD3	0	protein	778	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P06839
General transcription and DNA repair factor IIH subunit SSL1	6	protein	461	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q04673

Sequence of entity 1 (1), FASTA

>7K01_1 General transcription and DNA repair factor IIH subunit TFB1 (chains 1)
MSHSGAAIFEKVSGIIAINEDVSPAELTWRSTDGDKVHTVVLSTIDKLQATPASSEKMML
RLIGKVDESKKRKDNEGNEVVPKPQRHMFSFNNRTVMDNIKMTLQQIISRYKDADIYEEK
RRREESAQHTETPMSSSSVTAGTPTPHLDTPQLNNGAPLINTAKLDDSLSKEKLLTNLKL
QQSLLKGNKVLMKVFQETVINAGLPPSEFWSTRIPLLRAFALSTSQKVGPYNVLSTIKPV
ASSENKVNVNLSREKILNIFENYPIVKKAYTDNVPKNFKEPEFWARFFSSKLFRKLRGEK
IMQNDRGDVIIDRYLTLDQEFDRKDDDMLLHPVKKIIDLDGNIQDDPVVRGNRPDFTMQP
GVDINGNSDGTVDILKGMNRLSEKMIMALKNEYSRTNLQNKSNITNDEEDEDNDERNELK
IDDLNESYKTNYAIIHLKRNAHEKTTDNDAKSSADSIKNADLKVSNQQMLQQLSLVMDNL
INKLDLNQVVPNNEVSNKINKRVITAIKINAKQAKHNNVNSALGSFVDNTSQANELEVKS
TLPIDLLESCRMLHTTCCEFLKHFYIHFQSGEQKQASTVKKLYNHLKDCIEKLNELFQDV
LNGDGESMSNTCTAYLKPVLNSITLATHKYDEYFNEYNNNSN

Sequence of entity 2 (4), FASTA

>7K01_2 General transcription and DNA repair factor IIH subunit TFB4 (chains 4)
MDAISDPTFKHARSRKQVTEESPSLLTVIIEIAPKLWTTFDEEGNEKGSIIKVLEALIVF
LNAHLAFNSANKVAVIAAYSQGIKYLYPESTSALKASESENKTRSDLKIINSDMYRRFRN
VDETLVEEIYKLFELEKKQIEQNSQRSTLAGAMSAGLTYVNRISKESVTTSLKSRLLVLT
CGSGSSKDEIFQYIPIMNCIFSATKMKCPIDVVKIGGSKESTFLQQTTDATNGVYLHVES
TEGLIQYLATAMFIDPSLRPIIVKPNHGSVDFRTSCYLTGRVVAVGFICSVCLCVLSIIP
PGNKCPACDSQFDEHVIAKLKRKPVVPRLKAKKKVTKP

Sequence of entity 3 (7), FASTA

>7K01_3 DNA repair helicase RAD25 (chains 7)
MTDVEGYQPKSKGKIFPDMGESFFSSDEDSPATDAEIDENYDDNRETSEGRGERDTGAMV
TGLKKPRKKTKSSRHTAADSSMNQMDAKDKALLQDTNSDIPADFVPDSVSGMFRSHDFSY
LRLRPDHASRPLWISPSDGRIILESFSPLAEQAQDFLVTIAEPISRPSHIHEYKITAYSL
YAAVSVGLETDDIISVLDRLSKVPVAESIINFIKGATISYGKVKLVIKHNRYFVETTQAD
ILQMLLNDSVIGPLRIDSDHQVQPPEDVLQQQLQQTAGKPATNVNPNDVEAVFSAVIGGD
NEREEEDDDIDAVHSFEIANESVEVVKKRCQEIDYPVLEEYDFRNDHRNPDLDIDLKPST
QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGITAACTIKKSVIVLCTSSVSVMQW
RQQFLQWCTLQPENCAVFTSDNKEMFQTESGLVVSTYSMVANTRNRSHDSQKVMDFLTGR
EWGFIILDEVHVVPAAMFRRVVSTIAAHAKLGLTATLVREDDKIGDLNFLIGPKLYEANW
MELSQKGHIANVQCAEVWCPMTAEFYQEYLRETARKRMLLYIMNPTKFQACQFLIQYHER
RGDKIIVFSDNVYALQEYALKMGKPFIYGSTPQQERMNILQNFQYNDQINTIFLSKVGDT
SIDLPEATCLIQISSHYGSRRQEAQRLGRILRAKRRNDEGFNAFFYSLVSKDTQEMYYST
KRQAFLVDQGYAFKVITHLHGMENIPNLAYASPRERRELLQEVLLKNEEAAGIEVGDDAD
NSVGRGSNGHKRFKSKAVRGEGSLSGLAGGEDMAYMEYSTNKNKELKEHHPLIRKMYYKN
LKK

Sequence of entity 4 (5), FASTA

>7K01_4 RNA polymerase II transcription factor B subunit 5 (chains 5)
MARARKGALVQCDPSIKALILQIDAKMSDIVLEELDDTHLLVNPSKVEFVKHELNRLLSK
NIYNPMDEEENQ

Sequence of entity 5 (2), FASTA

>7K01_5 General transcription and DNA repair factor IIH subunit TFB2 (chains 2)
MSDYSLKHSVTQYLEEIPQQVQNRLYTSPATCLAIYRILPPLAKFFIMAMVFNENEVPLL
DLDKWVNSNGKLQFQNAIKSMKSLHLLIPNKSSGTLMINLNPTFKISLRNALTGGEVQNS
FGVVVEENVVSLDLLDEYSANKWETILHFMVGTPLAKIPSEKVLNLLKHSKLMEEVNSTG
EFKITNEGFQFLLQEINSQLWTLLLQYLKMIETSKMDLVDVLHFIFMLGALEVGKAYKID
ALSETQRIMLQDMRDYGLVFQKHSNDSIFYPTKLALMLTSDTKTIRSASNAMDSVLRQNR
EEPSVNEDGANGKSTTDITTSDDLNKAGLKNQDIPDGSLIVETNFKIYSYSNSPLQIAVL
SLFVHLKARFVNMVLGQITRESIRRALTNGITADQIIAYLETHAHPQMRRLAEEKLEKKL
ELDPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGV
LLWKDDKKKKFFISKEGNSQVLDFAKRKLKKKQ

Sequence of entity 6 (0), FASTA

>7K01_6 DNA repair helicase RAD3 (chains 0)
MKFYIDDLPVLFPYPKIYPEQYNYMCDIKKTLDVGGNSILEMPSGTGKTVSLLSLTIAYQ
MHYPEHRKIIYCSRTMSEIEKALVELENLMDYRTKELGYQEDFRGLGLTSRKNLCLHPEV
SKERKGTVVDEKCRRMTNGQAKRKLEEDPEANVELCEYHENLYNIEVEDYLPKGVFSFEK
LLKYCEEKTLCPYFIVRRMISLCNIIIYSYHYLLDPKIAERVSNEVSKDSIVIFDEAHNI
DNVCIESLSLDLTTDALRRATRGANALDERISEVRKVDSQKLQDEYEKLVQGLHSADILT
DQEEPFVETPVLPQDLLTEAIPGNIRRAEHFVSFLKRLIEYLKTRMKVLHVISETPKSFL
QHLKQLTFIERKPLRFCSERLSLLVRTLEVTEVEDFTALKDIATFATLISTYEEGFLLII
EPYEIENAAVPNPIMRFTCLDASIAIKPVFERFSSVIITSGTISPLDMYPRMLNFKTVLQ
KSYAMTLAKKSFLPMIITKGSDQVAISSRFEIRNDPSIVRNYGSMLVEFAKITPDGMVVF
FPSYLYMESIVSMWQTMGILDEVWKHKLILVETPDAQETSLALETYRKACSNGRGAILLS
VARGKVSEGIDFDHQYGRTVLMIGIPFQYTESRILKARLEFMRENYRIRENDFLSFDAMR
HAAQCLGRVLRGKDDYGVMVLADRRFSRKRSQLPKWIAQGLSDADLNLSTDMAISNTKQF
LRTMAQPTDPKDQEGVSVWSYEDLIKHQNSRKDQGGFIENENKEGEQDEDEDEDIEMQ

Sequence of entity 7 (6), FASTA

>7K01_7 General transcription and DNA repair factor IIH subunit SSL1 (chains 6)
MAPVVISESEEDEDRVAITRRTKRQVHFDGEGDDRVDQQQQQHSSSHRDRDKHVQRKKKK
RLSNRNLQGSNGGYAWEDEIKRSWDLVKVDDEGDMASLVASIVEARKKRTAKKNITPYQR
GIIRSLILTLDCSEAMLEKDLRPNRHAMIIQYAIDFVHEFFDQNPISQMGIIIMRNGLAQ
LVSQVSGNPQDHIDALKSIRKQEPKGNPSLQNALEMARGLLLPVPAHCTREVLIVFGSLS
TTDPGDIHQTIDSLVSEKIRVKVLGLSAQVAICKELCKATNYGDESFYKILLDETHLKEL
FNEAVTPLPVNKINKGFTLVKMGFPTRIFEDTPTFCSCHSKLVYGGYFCPNCHSKVCSLP
TVCPCCDLMLILSTHLARSYHHLMPLKTFAEVPTTEKFRSEDCFSCQSRFPILKNHKNGK
LLTSSRYRCEDCKQEFCVDCDVFIHEILHNCPGCESKPVIT

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	1
ZN	Zinc ion	Zn	5

Primary citation

Cryo-EM structure of TFIIH/Rad4-Rad23-Rad33 in damaged DNA opening in nucleotide excision repair. van Eeuwen, T., Shim, Y., Kim, H.J. et al. Nat Commun (2021) 12:3338-3338. DOI 10.1038/s41467-021-23684-x · PubMed

Other PDB entries of the same protein (UniProt P32776 (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…
7O4I 3.2 Å, Yeast RNA polymerase II transcription pre-initiation complex with initial transcription…
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

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