6NMI: Human TFIIH core complex

Cryo-EM structure of the human TFIIH core complex. Determined by electron microscopy at 3.7 Å resolution. Released 13 Mar 2019.

Method: Electron microscopy
Resolution: 3.7 Å
Organism: Homo sapiens
Chains: 8
Atoms: 24,379
Mol. weight: 389.39 kDa
Ligands: SF4, ZN
Released: 13 Mar 2019

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

Secondary structure: helices and β-sheets

6NMI contains 142 α-helices and 121 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, 31 β-strands

Element	Residues	Length	Sheet
α-helix	38-41	4
β-strand	53	1	1
β-strand	59-60	2	1
β-strand	76-78	3	2
β-strand	83-87	5	2
α-helix	93-103	11
β-strand	105-108	4	2
β-strand	113-117	5	2
α-helix	120-129	10
α-helix	133-141	9
β-strand	144	1	2
α-helix	150-160	11
β-strand	166-171	6	3
β-strand	174-179	6	3
α-helix	182-189	8
α-helix	192-197	6
β-strand	198	1	3
α-helix	249-261	13
β-strand	268-272	5	3
α-helix	274-276	3
α-helix	277-286	10
β-strand	291-293	3	3
β-strand	294-295	2	4
α-helix	304-305	2
β-strand	310	1	5
α-helix	318-327	10
β-strand	333-334	2	4
β-strand	336-339	4	6
α-helix	346-357	12
α-helix	360	1
β-strand	361-365	5	6
α-helix	368-379	12
β-strand	382	1	5
β-strand	406-409	4	6
α-helix	421-430	10
β-strand	437-441	5	6
α-helix	443-445	3
α-helix	448-458	11
β-strand	463-467	5	6
α-helix	480-483	4
β-strand	487-489	3	6
α-helix	493-495	3
β-strand	505-512	8	7
α-helix	516-524	9
α-helix	530-533	4
α-helix	538-552	15
β-strand	558-561	4	7
α-helix	565-575	11
β-strand	579-580	2	7
α-helix	586-597	12
β-strand	604-607	4	7
α-helix	609-611	3
β-strand	620	1	8
β-strand	622-625	4	7
α-helix	633-643	11
β-strand	644	1	8
β-strand	657-664	8	7
α-helix	669-683	15
β-strand	689-690	2	7
α-helix	707-717	11

Chain B: 35 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	9
β-strand	9-11	3	9
β-strand	17	1	10
α-helix	19-33	15
β-strand	39-40	2	11
α-helix	48-62	15
β-strand	69-73	5	12
α-helix	77-97	21
β-strand	106-108	3	12
α-helix	127-137	11
α-helix	142-147	6
α-helix	157-160	4
α-helix	161-165	5
β-strand	175	1	12
α-helix	177-183	7
α-helix	184-188	5
α-helix	191-197	7
β-strand	204-207	4	12
α-helix	223-226	4
β-strand	229-233	5	12
α-helix	239-247	9
β-strand	249-252	4	13
α-helix	253-276	24
α-helix	279-289	11
α-helix	326-344	19
β-strand	350-352	3	13
α-helix	354-364	11
α-helix	370-373	4
α-helix	375-385	11
α-helix	391-394	4
α-helix	395-407	13
β-strand	414-419	6	13
β-strand	432-437	6	13
α-helix	441-450	10
β-strand	455	1	12
β-strand	456-457	2	11
α-helix	468-471	4
β-strand	478	1	11
β-strand	479-481	3	14
β-strand	490-494	5	15
β-strand	495	1	16
α-helix	514-530	17
β-strand	535-539	5	15
α-helix	542-550	9
α-helix	558-564	7
β-strand	566-569	4	15
α-helix	576-587	12
β-strand	594-599	6	15
α-helix	603-605	3
β-strand	617-621	5	15
α-helix	631-642	12
α-helix	648-664	17
β-strand	675-680	6	15
α-helix	682-685	4
α-helix	690-692	3
α-helix	695-698	4
β-strand	708	1	16
α-helix	710-723	14
α-helix	730-732	3
β-strand	739	1	10
α-helix	747-756	10
β-strand	757-759	3	14

Chain C: 17 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	109-120	12
α-helix	122-128	7
α-helix	129-133	5
α-helix	139-144	6
α-helix	190-199	10
α-helix	201-209	9
α-helix	217-222	6
α-helix	241-252	12
α-helix	253-257	5
α-helix	296-317	22
α-helix	347-358	12
β-strand	373	1	17
α-helix	380-383	4
α-helix	398-410	13
α-helix	424-434	11
α-helix	455-479	25
α-helix	486-514	29
α-helix	523-545	23

Chain D: 22 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	20-23	4
α-helix	28-34	7
α-helix	38-45	8
α-helix	50-59	10
β-strand	66	1	18
α-helix	68-72	5
β-strand	75	1	19
α-helix	77-79	3
α-helix	84-92	9
β-strand	96-100	5	18
β-strand	106-110	5	18
α-helix	112-122	11
α-helix	142-144	3
α-helix	145-164	20
α-helix	175-181	7
β-strand	187	1	20
β-strand	194	1	20
α-helix	198-204	7
α-helix	208-220	13
α-helix	230-240	11
α-helix	256-268	13
β-strand	271-273	3	21
β-strand	281-283	3	21
α-helix	285-288	4
β-strand	307-310	4	1
β-strand	314-317	4	1
α-helix	322-331	10
β-strand	333-337	5	1
β-strand	342-345	4	1
α-helix	348-356	9
α-helix	363-370	8
β-strand	372	1	1
α-helix	385-398	14
β-strand	402-405	4	22
β-strand	407-410	4	23
α-helix	416-427	12
β-strand	431-433	3	23
β-strand	440-443	4	23
α-helix	448-455	8

Chain E: 16 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	30-41	12
β-strand	53	1	17
β-strand	55	1	24
β-strand	60	1	25
β-strand	61-66	6	26
α-helix	70-72	3
α-helix	80-98	19
β-strand	103	1	25
β-strand	104-110	7	26
β-strand	113-121	9	26
α-helix	124-134	11
α-helix	145-155	11
β-strand	166-171	6	26
α-helix	184-191	8
β-strand	195-200	6	26
α-helix	206-215	10
β-strand	219-221	3	26
α-helix	225-234	10
α-helix	238-239	2
β-strand	240	1	24
α-helix	241	1
β-strand	249-253	5	27
α-helix	255-256	2
β-strand	257-258	2	28
β-strand	270	1	29
β-strand	285	1	29
β-strand	288-289	2	28
β-strand	298	1	28
β-strand	304	1	27
β-strand	311-312	2	27
α-helix	319-321	3
β-strand	332-334	3	30
β-strand	344	1	31
β-strand	351	1	31
β-strand	357-359	3	30
β-strand	366-367	2	30
α-helix	369-374	6
α-helix	375-379	5
α-helix	383-386	4

Chain F: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	10-16	7	32
α-helix	19-27	9
α-helix	34-51	18
β-strand	56-62	7	32
β-strand	67-71	5	32
α-helix	102-119	18
α-helix	134-149	16
β-strand	159-165	7	32
α-helix	168-170	3
α-helix	171-173	3
α-helix	174-186	13
β-strand	190-195	6	32
α-helix	201-209	9
β-strand	213-216	4	32
α-helix	220-222	3
α-helix	223-226	4
α-helix	227-231	5
α-helix	235-238	4
β-strand	241	1	19
α-helix	244-250	7
β-strand	254	1	33
β-strand	261	1	33
β-strand	264-268	5	27
β-strand	274-275	2	27
β-strand	282	1	34
β-strand	287	1	34

Chain G: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	22
α-helix	14-26	13
β-strand	34	1	22
β-strand	43-45	3	22
α-helix	47-49	3
α-helix	50-64	15

Chain H: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
β-strand	21-23	3	35
β-strand	31	1	35
α-helix	32-39	8
β-strand	45	1	36
β-strand	52	1	36
β-strand	59-61	3	35
α-helix	66-79	14
α-helix	92-111	20
α-helix	114-129	16
α-helix	132-188	57
α-helix	194-209	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
General transcription and DNA repair factor IIH helicase subunit XPB	A	protein	653	Homo sapiens	P19447 (AlphaFold model)
General transcription and DNA repair factor IIH helicase subunit XPD	B	protein	760	Homo sapiens	P18074 (AlphaFold model)
General transcription factor IIH subunit 1, p62	C	protein	548	Homo sapiens	P32780 (AlphaFold model)
General transcription factor IIH subunit 4, p52	D	protein	462	Homo sapiens	Q92759 (AlphaFold model)
General transcription factor IIH subunit 2, p44	E	protein	366	Homo sapiens	Q13888
General transcription factor IIH subunit 3, p34	F	protein	308	Homo sapiens	Q13889
General transcription factor IIH subunit 5, p8	G	protein	71	Homo sapiens	Q6ZYL4
CDK-activating kinase assembly factor MAT1	H	protein	309	Homo sapiens	P51948

Sequence of entity 1 (A), FASTA

>6NMI_1 General transcription and DNA repair factor IIH helicase subunit XPB (chains A)
PQEAVPSAAGKQVDESGTKVDEYGAKDYRLQMPLKDDHTSRPLWVAPDGHIFLEAFSPVY
KYAQDFLVAIAEPVCRPTHVHEYKLTAYSLYAAVSVGLQTSDITEYLRKLSKTGVPDGIM
QFIKLCTVSYGKVKLVLKHNRYFVESCHPDVIQHLLQDPVIRECRLRNSEXXXXXXXXXX
XXXXXXXXQTVSFEVKQEMIEELQKRCIHLEYPLLAEYDFRNDSVNPDINIDLKPTAVLR
PYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQ
FKMWSTIDDSQICRFTSDAKDKPIGCSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGL
MILDEVHTIPAKMFRRVLTIVQAHCKLGLTATLVREDDKIVDLNFLIGPKLYEANWMELQ
NNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNKFRACQFLIKFHERRNDK
IIVFADNVFALKEYAIRLNKPYIYGPTSQGERMQILQNFKHNPKINTIFISKVGDTSFDL
PEANVLIQISSHGGSRRQEAQRLGRVLRAKKGMVAEEYNAFFYSLVSQDTQEMAYSTKRQ
RFLVDQGYSFKVITKLAGMEEEDLAFSTKEEQQQLLQKVLAATDLDAEEEVVA

Sequence of entity 2 (B), FASTA

>6NMI_2 General transcription and DNA repair factor IIH helicase subunit XPD (chains B)
MKLNVDGLLVYFPYDYIYPEQFSYMRELKRTLDAKGHGVLEMPSGTGKTVSLLALIMAYQ
RAYPLEVTKLIYCSRTVPEIEKVIEELRKLLNFYEKQEGEKLPFLGLALSSRKNLCIHPE
VTPLRFGKDVDGKCHSLTASYVRAQYQHDTSLPHCRFYEEFDAHGREVPLPAGIYNLDDL
KALGRRQGWCPYFLARYSILHANVVVYSYHYLLDPKIADLVSKELARKAVVVFDEAHNID
NVCIDSMSVNLTRRTLDRCQGNLETLQKTVLRIKETDEQRLRDEYRRLVEGXXXXXXXXX
XXXXXXXXXXXXXXXXXXVPGSIRTAEHFLGFLRRLLEYVKWRLRVQHVVQESPPAFLSG
LAQRVCIQRKPLRFCAERLRSLLHTLEITDLADFSPLTLLANFATLVSTYAKGFTIIIEP
FDDRTPTIANPILHFSCMDASLAIKPVFERFQSVIITSGTLSPLDIYPKILDFHPVTMAT
FTMTLARVCLCPMIIGRGNDQVAISSKFETREDIAVIRNYGNLLLEMSAVVPDGIVAFFT
SYQYMESTVASWYEQGILENIQRNKLLFIETQDGAETSVALEKYQEACENGRGAILLSVA
RGKVSEGIDFVHHYGRAVIMFGVPYVYTQSRILKARLEYLRDQFQIRENDFLTFDAMRHA
AQCVGRAIRGKTDYGLMVFADKRFARGDKRGKLPRWIQEHLTDANLNLTVDEGVQVAKYF
LRQMAQPFHREDQLGLSLLSLEQLESEETLKRIEQIAQQL

Sequence of entity 3 (C), FASTA

>6NMI_3 General transcription factor IIH subunit 1, p62 (chains C)
MATSSEEVLLIVKKVRQKKQDGALYLMAERIAWAPEGKDRFTISHMYADIKCQKISPEGK
AKIQLQLVLHAGDTTNFHFSNESTAVKERDAVKDLLQQLLPKFKRKANKELEEKNRMLQE
DPVLFQLYKDLVVSQVISAEEFWANRLXXXXXXXXXXXXXXXXXXXXXXXXXXVRPQTDG
CNXXXXXXXSDIIESIFRTYPAVKMKYAENVPHNMTEKEFWTRFFQSHYFHRXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXENSN
AAIIKRFNHHSAMVLAAGLRKQEAQNEQTSEPSNMDGNSGDADCFQPAVKRAKLQESIEY
EDLGXXXXXXXIALNLKKSDRYYHGPTPIXXXXXXTSQDIINSFQSIRQEMEAYTPKLTQ
VLSSSAASSTITALSPGGALMQXXXXXXXXXXVPNDIQSELKHLYVAVGELLRHFWSCFX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLVSHIEEMLQTAYNKLHTWX
XXXXXXXT

Sequence of entity 4 (D), FASTA

>6NMI_4 General transcription factor IIH subunit 4,  p52 (chains D)
MESTPSRGLNRVHLQCRNLQEFLGGLSPGVLDRLYGHPATCLAVFRELPSLAKNWVMRML
FLEQPLPQAAVALWVKKEFSKAQEESTGLLSGLRIWHTQLLPGGLQGLILNPIFRQNLRI
ALLGGGKAWSDDTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQLLS
QAGLMKSTEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQL
SFSTLGKDYSVEGMSDSLLNFLQHLREFGLVFQRKRKSRRYYPTRLAINLSSGVSGAGGT
VHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGIT
AQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFEL
LLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQKHSS

Sequence of entity 5 (E), FASTA

>6NMI_5 General transcription factor IIH subunit 2, p44 (chains E)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXGQVRLGMMRHLYVVVDGSRTMEDQD
LKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKKAV
DMTCHGEPSLYNSLSIAMQTLKHMPGHTSREVLIIFSSLTTCDPSNIYDLIKTLKAAKIR
VSVIGLSAEVRVCTVLARETGGTYHVILDESHYKELLTHHVSPPPASSSSECSLIRMGFP
QHTIXXXXXXXXXXXXXXXXXXXXXGGYFCPQCRAKYCELPVECKICGLTLVSAPHLARS
YHHLFPLDAFQEIPLEEYNGERFCYGCQGELKDQHVYVCAVCQNVFCVDCDVFVHDSLHC
CPGCIH

Sequence of entity 6 (F), FASTA

>6NMI_6 General transcription factor IIH subunit 3, p34 (chains F)
MVSDEDELNLLVIVVDANPIWWGKQALKESQFTLSKCIDAVMVLGNSHLFMNRSNKLAVI
ASHIQESRFLYPGKNGRLGDFFGDPGNPPEFNPSGSKDGKYELLTSANEVIVEEIKDLMT
KSDIKGQHTETLLAGSLAKALCYIHRMNKEVKDNQEMKSRILVIKAAEDSALQYMNFMNV
IFAAQKQNILIDACVLDSDSGLLQQACDITGGLYLKVPQMPSLLQYLLWVFLPDQDQRSQ
LILPPPVHVDYRAACFCHRNLIEIGYVCSVCLSIFCNFSPICTTCETAFKISLPPVLKAK
KKKLKVSA

Sequence of entity 7 (G), FASTA

>6NMI_7 General transcription factor IIH subunit 5, p8 (chains G)
MVNVLKGVLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGEL
MDQNAFSLTQK

Sequence of entity 8 (H), FASTA

>6NMI_8 CDK-activating kinase assembly factor MAT1 (chains H)
MDDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRV
QLFEDPTVDKEVEIRKKVLKIYNKREEDFPSLREYNDFLEEVEEIVFNLTNNVDLDNTKK
KMEIYQKENKDVIQKNKLKLTREQEELEEALEVERQENEQRRLFIQKEEQLQQILKRKNK
QAFLDELESSDLPVALLLAQHKDRSTQLEMQLEKPKPVKPVTFSTGIKMGQHISLAPIHK
LEEALYEYQPLQIETYGPHVPELEMLGRLGYLNHVRAASPQDLAGGYTSSLACHRALQDA
FSGLFWQPS

Ligands and cofactors

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

Primary citation

The complete structure of the human TFIIH core complex. Greber, B.J., Toso, D.B., Fang, J. et al. Elife (2019) 8. DOI 10.7554/eLife.44771 · 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
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

Browse structure collections

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