6RO4: Core TFIIH-XPA-DNA complex

Structure of the core TFIIH-XPA-DNA complex. Determined by electron microscopy at 3.5 Å resolution. Released 3 Jul 2019.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 9
Atoms: 19,827
Mol. weight: 377.91 kDa
Ligands: SF4, ZN
Released: 3 Jul 2019

Explore 6RO4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6RO4 contains 118 α-helices and 95 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 A: 26 helices, 31 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	141-143	3
α-helix	153-158	6
β-strand	167-170	4	2
β-strand	175-179	5	2
α-helix	185-188	4
β-strand	198	1	2
β-strand	268-272	5	2
α-helix	278-286	9
β-strand	295	1	3
α-helix	315-317	3
α-helix	320-327	8
β-strand	333	1	3
β-strand	337-339	3	4
α-helix	348-357	10
β-strand	361-364	4	4
α-helix	370-381	12
β-strand	389-391	3	4
β-strand	405-407	3	4
α-helix	421-430	10
β-strand	435	1	5
β-strand	438-441	4	4
α-helix	443-445	3
α-helix	454-457	4
β-strand	460	1	5
β-strand	463-467	5	4
α-helix	480-483	4
β-strand	487-490	4	4
α-helix	495-498	4
β-strand	505	1	6
β-strand	508-510	3	7
β-strand	511-512	2	8
α-helix	513-515	3
α-helix	518-522	5
α-helix	530-533	4
α-helix	538-552	15
β-strand	558-559	2	7
β-strand	562	1	7
α-helix	566-572	7
β-strand	579-580	2	9
α-helix	587-597	11
β-strand	606-607	2	9
β-strand	622-626	5	7
α-helix	635-637	3
α-helix	640-643	4
β-strand	657	1	6
β-strand	658-662	5	7
β-strand	663-664	2	8
α-helix	669-675	7
β-strand	688-690	3	7
α-helix	707-716	10

Chain B: 31 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	12
β-strand	9-11	3	12
α-helix	19-34	16
β-strand	38-41	4	13
α-helix	48-62	15
β-strand	69-73	5	13
α-helix	77-98	22
β-strand	106-108	3	13
α-helix	127-138	12
α-helix	145-147	3
α-helix	156-159	4
α-helix	177-187	11
α-helix	191-197	7
β-strand	204-207	4	13
α-helix	209-211	3
α-helix	215-221	7
β-strand	229-234	6	13
α-helix	240-245	6
β-strand	249-252	4	14
α-helix	253-270	18
α-helix	327-344	18
β-strand	351-352	2	14
α-helix	357-360	4
α-helix	369-372	4
α-helix	375-386	12
α-helix	395-409	15
β-strand	414-419	6	14
β-strand	432-437	6	14
α-helix	447-450	4
β-strand	453-458	6	13
α-helix	467-470	4
β-strand	480	1	13
β-strand	490-493	4	15
β-strand	495	1	16
α-helix	514-527	14
β-strand	535-539	5	15
α-helix	543-552	10
α-helix	558-564	7
β-strand	566-569	4	15
α-helix	574-587	14
β-strand	594-599	6	15
α-helix	603-606	4
β-strand	617-620	4	15
α-helix	633-642	10
α-helix	648-656	9
α-helix	665-667	3
β-strand	675-679	5	15
α-helix	682-685	4
α-helix	687-690	4
α-helix	695-698	4
β-strand	708	1	16
α-helix	710-724	15

Chain C: 27 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	19-24	6
α-helix	28-34	7
α-helix	39-46	8
α-helix	52-58	7
α-helix	65-67	3
α-helix	72-74	3
β-strand	75	1	18
α-helix	81-92	12
β-strand	96	1	25
α-helix	109	1
β-strand	110	1	25
α-helix	111	1
α-helix	112-121	10
α-helix	146-160	15
α-helix	161-163	3
α-helix	173-182	10
α-helix	198-204	7
α-helix	208-220	13
α-helix	223-226	4
α-helix	230-240	11
α-helix	256-268	13
α-helix	285-288	4
β-strand	308-309	2	26
β-strand	314-317	4	26
α-helix	322-328	7
β-strand	333-338	6	26
β-strand	341-345	5	26
α-helix	348-355	8
α-helix	361-370	10
α-helix	381	1
α-helix	385-399	15
β-strand	402	1	11
β-strand	407-409	3	10
α-helix	417-420	4
β-strand	431-433	3	10
β-strand	441-443	3	10
α-helix	445-447	3
α-helix	452-457	6

Chain D: 16 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	59-66	8	22
α-helix	69-72	4
α-helix	80-98	19
β-strand	103-109	7	22
β-strand	114-121	8	22
α-helix	128-131	4
α-helix	133-136	4
α-helix	146-154	9
β-strand	164-171	8	22
α-helix	182-184	3
α-helix	185-191	7
β-strand	195-200	6	22
α-helix	206-215	10
β-strand	219-221	3	22
α-helix	225-233	9
α-helix	238-239	2
β-strand	279-280	2	21
β-strand	282	1	23
β-strand	283	1	20
β-strand	290	1	24
β-strand	297	1	24
α-helix	303	1
β-strand	304	1	23
α-helix	305	1
β-strand	311	1	23
α-helix	315-319	5
α-helix	327-330	4
α-helix	369-374	6
α-helix	375-379	5

Chain E: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	10-16	7	17
α-helix	19-28	10
α-helix	35-48	14
β-strand	56-62	7	17
β-strand	69	1	17
α-helix	105-118	14
α-helix	133-147	15
β-strand	159-165	7	17
α-helix	168-170	3
α-helix	171-173	3
α-helix	174-185	12
β-strand	190-195	6	17
α-helix	201-209	9
β-strand	214-216	3	17
α-helix	223-230	8
α-helix	235-240	6
β-strand	241	1	18
α-helix	244-246	3
β-strand	253-254	2	19
β-strand	261-262	2	19
β-strand	264	1	20
β-strand	266-268	3	21
β-strand	274-275	2	21

Chain F: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	10
β-strand	8-11	4	11
α-helix	14-24	11
β-strand	34-37	4	11
β-strand	42-45	4	11
α-helix	48-50	3
α-helix	54-63	10

Chain G: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	138-140	3	27
α-helix	141-147	7
α-helix	161-162	2
β-strand	165-168	4	27
β-strand	177-182	6	27
α-helix	183-193	11
α-helix	198-235	38

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA1	J	DNA	49	Homo sapiens
DNA2	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

Sequence of entity 1 (J), FASTA

>6RO4_1 DNA1 (chains J)
CAAAGTCACGACCTAGACACTGCGAGCTCGAATTCACTGGAGTGACCTC

Sequence of entity 2 (K), FASTA

>6RO4_2 DNA2 (chains K)
GAGGTCACTCCAGTGAATTCGAGCTCGCAACAATGAGCACATACCTAGT

Sequence of entity 3 (A), FASTA

>6RO4_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

>6RO4_4 General transcription factor IIH subunit 5 (chains F)
MVNVLKGVLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGEL
MDQNAFSLTQK

Sequence of entity 5 (B), FASTA

>6RO4_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

>6RO4_6 General transcription factor IIH subunit 3 (chains E)
MVSDEDELNLLVIVVDANPIWWGKQALKESQFTLSKCIDAVMVLGNSHLFMNRSNKLAVI
ASHIQESRFLYPGKNGRLGDFFGDPGNPPEFNPSGSKDGKYELLTSANEVIVEEIKDLMT
KSDIKGQHTETLLAGSLAKALCYIHRMNKEVKDNQEMKSRILVIKAAEDSALQYMNFMNV
IFAAQKQNILIDACVLDSDSGLLQQACDITGGLYLKVPQMPSLLQYLLWVFLPDQDQRSQ
LILPPPVHVDYRAACFCHRNLIEIGYVCSVCLSIFCNFSPICTTCETAFKISLPPVLKAK
KKKLKVSA

Sequence of entity 7 (D), FASTA

>6RO4_7 General transcription factor IIH subunit 2 (chains D)
MDEEPERTKRWEGGYERTWEILKEDESGSLKATIEDILFKAKRKRVFEHHGQVRLGMMRH
LYVVVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTEL
SGNPRKHITSLKKAVDMTCHGEPSLYNSLSIAMQTLKHMPGHTSREVLIIFSSLTTCDPS
NIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETGGTYHVILDESHYKELLTHHVSPPP
ASSSSECSLIRMGFPQHTIASLSDQDAKPSFSMAHLDGNTEPGLTLGGYFCPQCRAKYCE
LPVECKICGLTLVSAPHLARSYHHLFPLDAFQEIPLEEYNGERFCYGCQGELKDQHVYVC
AVCQNVFCVDCDVFVHDSLHCCPGCIHKIPAPSGV

Sequence of entity 8 (C), FASTA

>6RO4_8 General transcription factor IIH subunit 4 (chains C)
MESTPSRGLNRVHLQCRNLQEFLGGLSPGVLDRLYGHPATCLAVFRELPSLAKNWVMRML
FLEQPLPQAAVALWVKKEFSKAQEESTGLLSGLRIWHTQLLPGGLQGLILNPIFRQNLRI
ALLGGGKAWSDDTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQLLS
QAGLMKSTEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQL
SFSTLGKDYSVEGMSDSLLNFLQHLREFGLVFQRKRKSRRYYPTRLAINLSSGVSGAGGT
VHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGIT
AQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFEL
LLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQKHSS

Sequence of entity 9 (G), FASTA

>6RO4_9 DNA repair protein complementing XP-A cells (chains G)
MAAADGALPEAAALEQPAELPASVRASIERKRQRALMLRQARLAARPYSATAAAATGGMA
NVKAAPKIIDTGGGFILEEEEEEEQKIGKVVHQPGPVMEFDYVICEECGKEFMDSYLMNH
FDLPTCDNCRDADDKHKLITKTEAKQEYLLKDCDLEKREPPLKFIVKKNPHHSQWGDMKL
YLKLQIVKRSLEVWGSQEALEEAKEVRQENREKMKQKKFDKKVKELRRAVRSSVWKRETI
VHQHEYGPEENLEDDMYRKTCTMCGHELTYEKM

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	1
ZN	Zinc ion	Zn	6

Primary citation

Structural basis of TFIIH activation for nucleotide excision repair. Kokic, G., Chernev, A., Tegunov, D. et al. Nat Commun (2019) 10:2885-2885. DOI 10.1038/s41467-019-10745-5 · 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
7AD8 3.5 Å, Core TFIIH-XPA-DNA complex with modelled p62 subunit
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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