28JM: PDB entry 28JM

Cryo-EM structure of the human holo-TFIIH and XPC initial encounter complex. Determined by electron microscopy at 3.29 Å resolution. Released 6 May 2026.

Method: Electron microscopy
Resolution: 3.29 Å
Organism: Homo sapiens
Chains: 9
Atoms: 25,112
Mol. weight: 528.04 kDa
Ligands: ZN, SF4
Released: 6 May 2026

Explore 28JM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

28JM contains 154 α-helices and 137 β-strands across 9 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: 34 helices, 41 β-strands

Element	Residues	Length	Sheet
α-helix	39-41	3
β-strand	42	1	1
β-strand	52-53	2	2
β-strand	59-60	2	2
α-helix	66-68	3
α-helix	71-73	3
β-strand	78	1	3
β-strand	84-87	4	3
α-helix	93-103	11
β-strand	105-108	4	3
β-strand	113-117	5	3
α-helix	120-128	9
α-helix	133-143	11
α-helix	150-158	9
β-strand	166-167	2	4
β-strand	169-171	3	5
β-strand	174-176	3	5
β-strand	179	1	4
α-helix	182-189	8
α-helix	192-196	5
β-strand	198	1	6
α-helix	251-263	13
β-strand	268	1	4
β-strand	271	1	5
β-strand	272	1	6
α-helix	274-276	3
α-helix	277-286	10
α-helix	290	1
β-strand	291-292	2	4
α-helix	293	1
β-strand	294-295	2	5
α-helix	297-299	3
α-helix	304-306	3
β-strand	310	1	7
α-helix	318-327	10
β-strand	333-334	2	5
β-strand	336-339	4	8
α-helix	346-357	12
β-strand	361-365	5	8
α-helix	368-381	14
β-strand	382	1	7
α-helix	386-388	3
β-strand	389-391	3	8
β-strand	392	1	9
β-strand	397	1	9
β-strand	405-409	5	8
α-helix	422-432	11
β-strand	435	1	10
β-strand	437-440	4	8
α-helix	448-457	10
β-strand	460	1	10
β-strand	463-467	5	8
β-strand	478	1	1
α-helix	480-483	4
β-strand	487-490	4	8
α-helix	493-499	7
β-strand	505-511	7	11
α-helix	513-515	3
α-helix	516-521	6
α-helix	529-535	7
α-helix	538-552	15
β-strand	558-561	4	11
α-helix	565-574	10
β-strand	580	1	11
α-helix	586-597	12
β-strand	604-607	4	11
β-strand	620	1	12
β-strand	622-625	4	11
α-helix	633-643	11
β-strand	644	1	12
β-strand	657-663	7	11
α-helix	669-682	14
β-strand	689-690	2	11
α-helix	706-717	12
α-helix	775-779	5

Chain B: 38 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	13
β-strand	8-11	4	13
β-strand	17	1	14
α-helix	19-34	16
β-strand	37-41	5	15
α-helix	48-62	15
β-strand	70-74	5	15
α-helix	77-98	22
β-strand	105-108	4	15
α-helix	127-137	11
α-helix	140-146	7
α-helix	156-164	9
α-helix	169-171	3
β-strand	173-174	2	15
α-helix	179-187	9
α-helix	191-198	8
β-strand	204-208	5	15
α-helix	209-211	3
α-helix	224-226	3
β-strand	230-234	5	15
α-helix	239-246	8
β-strand	249-251	3	16
α-helix	253-275	23
α-helix	279-289	11
α-helix	311-313	3
α-helix	318-320	3
α-helix	321-323	3
α-helix	326-343	18
β-strand	350-352	3	16
α-helix	354-365	12
α-helix	370-386	17
α-helix	395-407	13
β-strand	414-419	6	16
β-strand	432-437	6	16
α-helix	445-449	5
β-strand	453-458	6	15
α-helix	466-470	5
β-strand	477-480	4	15
β-strand	490-494	5	17
β-strand	495-497	3	18
α-helix	502	1
β-strand	503	1	18
α-helix	504	1
α-helix	514-530	17
β-strand	534-539	6	17
α-helix	542-554	13
α-helix	557-564	8
β-strand	567-569	3	17
α-helix	576-589	14
β-strand	594-599	6	17
β-strand	617-621	5	17
α-helix	630-642	13
α-helix	648-663	16
β-strand	675-679	5	17
α-helix	682-685	4
α-helix	687-690	4
α-helix	695-698	4
β-strand	708-709	2	18
α-helix	710-724	15
α-helix	730-732	3
β-strand	739	1	14
α-helix	741-744	4
α-helix	747-756	10
β-strand	758-759	2	15

Chain C: 20 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	116-120	5
α-helix	122-128	7
α-helix	129-133	5
α-helix	139-145	7
β-strand	186-188	3	19
α-helix	190-199	10
α-helix	201-209	9
α-helix	217-224	8
α-helix	244-260	17
α-helix	265-267	3
α-helix	295-318	24
α-helix	347-357	11
β-strand	373	1	20
α-helix	380-384	5
α-helix	388-389	2
α-helix	397-412	16
α-helix	424-434	11
α-helix	455-477	23
α-helix	484-500	17
α-helix	501-505	5
α-helix	506-515	10
α-helix	523-547	25

Chain D: 23 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	19-24	6
α-helix	28-34	7
α-helix	38-47	10
α-helix	50-58	9
β-strand	66-67	2	21
α-helix	68-72	5
β-strand	75	1	22
α-helix	81-92	12
β-strand	96	1	23
β-strand	99-100	2	21
β-strand	106-108	3	21
β-strand	110	1	23
α-helix	112-122	11
α-helix	137-139	3
α-helix	145-163	19
α-helix	173-181	9
β-strand	185-186	2	24
β-strand	195-196	2	24
α-helix	200-205	6
α-helix	208-221	14
α-helix	230-240	11
β-strand	249-250	2	25
α-helix	256-268	13
β-strand	271-272	2	26
β-strand	280-281	2	25
β-strand	282-283	2	26
α-helix	285-288	4
α-helix	294-296	3
β-strand	307-309	3	2
β-strand	315-317	3	2
α-helix	322-329	8
β-strand	333-337	5	2
β-strand	342-345	4	2
α-helix	348-356	9
α-helix	361-370	10
α-helix	374-378	5
α-helix	385-398	14
β-strand	403-409	7	27
α-helix	415-428	14
β-strand	431-433	3	27
β-strand	441-443	3	27
α-helix	447-457	11

Chain E: 19 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	31-42	12
β-strand	53	1	20
β-strand	55	1	28
β-strand	59-60	2	29
β-strand	63-66	4	30
α-helix	69-72	4
α-helix	80-98	19
β-strand	102-103	2	29
β-strand	104-110	7	30
β-strand	113-121	9	30
α-helix	124-133	10
α-helix	145-156	12
β-strand	164-165	2	29
β-strand	166-171	6	30
α-helix	182-192	11
β-strand	195-200	6	30
α-helix	206-215	10
β-strand	219-221	3	30
α-helix	225-236	12
α-helix	238-239	2
β-strand	240	1	28
α-helix	241	1
β-strand	250-253	4	31
α-helix	255-257	3
β-strand	258	1	32
β-strand	270	1	33
α-helix	273-276	4
β-strand	285	1	33
β-strand	288	1	32
β-strand	289-290	2	34
β-strand	297-298	2	34
β-strand	303-304	2	31
β-strand	311-312	2	31
α-helix	315-319	5
α-helix	322-324	3
α-helix	327-331	5
β-strand	332-335	4	35
β-strand	344	1	36
β-strand	351	1	36
β-strand	356-359	4	35
β-strand	366-367	2	35
α-helix	369-374	6
α-helix	375-379	5
α-helix	383-386	4

Chain F: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	9-16	8	37
α-helix	19-27	9
α-helix	34-51	18
β-strand	56-62	7	37
β-strand	67-71	5	37
α-helix	102-120	19
α-helix	133-150	18
β-strand	158-165	8	37
α-helix	175-186	12
β-strand	190-195	6	37
α-helix	201-210	10
β-strand	214-216	3	37
α-helix	223-226	4
α-helix	227-231	5
α-helix	235-240	6
β-strand	241	1	22
α-helix	244-248	5
β-strand	253-254	2	38
β-strand	261-262	2	38
β-strand	264-267	4	31
β-strand	274-275	2	31
β-strand	281	1	39
β-strand	288	1	39
α-helix	289-290	2

Chain G: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	4-11	8	27
α-helix	14-26	13
β-strand	36-37	2	27
β-strand	42-45	4	27
α-helix	50-63	14

Chain H: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
β-strand	21	1	40
β-strand	23-24	2	41
β-strand	31	1	40
α-helix	32-39	8
β-strand	45	1	42
β-strand	52	1	42
β-strand	58-59	2	41
α-helix	66-81	16
α-helix	92-110	19
α-helix	115-128	14
α-helix	131-189	59
α-helix	194-209	16

1 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 XPB	A	protein	797	Homo sapiens	P19447 (AlphaFold model)
TFIIH basal transcription factor complex helicase XPD subunit	B	protein	771	Homo sapiens	P18074 (AlphaFold model)
General transcription factor IIH subunit 1	C	protein	591	Homo sapiens	P32780 (AlphaFold model)
General transcription factor IIH subunit 4	D	protein	462	Homo sapiens	Q92759 (AlphaFold model)
General transcription factor IIH subunit 2	E	protein	395	Homo sapiens	Q13888
General transcription factor IIH subunit 3	F	protein	308	Homo sapiens	Q13889
General transcription factor IIH subunit 5	G	protein	71	Homo sapiens	Q6ZYL4
CDK-activating kinase assembly factor MAT1	H	protein	309	Homo sapiens	P51948
DNA repair protein complementing XP-C cells	I	protein	940	Homo sapiens	Q01831

Sequence of entity 1 (A), FASTA

>28JM_1 General transcription and DNA repair factor IIH helicase subunit XPB (chains A)
HHHHHHENLYFQSNAMGKRDRADRDKKKSRKRHYEDEEDDEEDAPGNDPQEAVPSAAGKQ
VDESGTKVDEYGAKDYRLQMPLKDDHTSRPLWVAPDGHIFLEAFSPVYKYAQDFLVAIAE
PVCRPTHVHEYKLTAYSLYAAVSVGLQTSDITEYLRKLSKTGVPDGIMQFIKLCTVSYGK
VKLVLKHNRYFVESCHPDVIQHLLQDPVIRECRLRNSEGEATELITETFTSKSAISKTAE
SSGGPSTSRVTDPQGKSDIPMDLFDFYEQMDKDEEEEEETQTVSFEVKQEMIEELQKRCI
HLEYPLLAEYDFRNDSVNPDINIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAG
KSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDDSQICRFTSDAKDKPIGCSV
AISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLG
LTATLVREDDKIVDLNFLIGPKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFYREYVAI
KTKKRILLYTMNPNKFRACQFLIKFHERRNDKIIVFADNVFALKEYAIRLNKPYIYGPTS
QGERMQILQNFKHNPKINTIFISKVGDTSFDLPEANVLIQISSHGGSRRQEAQRLGRVLR
AKKGMVAEEYNAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEEDLAFST
KEEQQQLLQKVLAATDLDAEEEVVAGEFGSRSSQASRRFGTMSSMSGADDTVYMEYHSSR
SKAPSKHVHPLFKRFRK

Sequence of entity 2 (B), FASTA

>28JM_2 TFIIH basal transcription factor complex helicase XPD subunit (chains B)
MKLNVDGLLVYFPYDYIYPEQFSYMRELKRTLDAKGHGVLEMPSGTGKTVSLLALIMAYQ
RAYPLEVTKLIYCSRTVPEIEKVIEELRKLLNFYEKQEGEKLPFLGLALSSRKNLCIHPE
VTPLRFGKDVDGKCHSLTASYVRAQYQHDTSLPHCRFYEEFDAHGREVPLPAGIYNLDDL
KALGRRQGWCPYFLARYSILHANVVVYSYHYLLDPKIADLVSKELARKAVVVFDEAHNID
NVCIDSMSVNLTRRTLDRCQGNLETLQKTVLRIKETDEQRLRDEYRRLVEGLREASAARE
TDAHLANPVLPDEVLQEAVPGSIRTAEHFLGFLRRLLEYVKWRLRVQHVVQESPPAFLSG
LAQRVCIQRKPLRFCAERLRSLLHTLEITDLADFSPLTLLANFATLVSTYAKGFTIIIEP
FDDRTPTIANPILHFSCMDASLAIKPVFERFQSVIITSGTLSPLDIYPKILDFHPVTMAT
FTMTLARVCLCPMIIGRGNDQVAISSKFETREDIAVIRNYGNLLLEMSAVVPDGIVAFFT
SYQYMESTVASWYEQGILENIQRNKLLFIETQDGAETSVALEKYQEACENGRGAILLSVA
RGKVSEGIDFVHHYGRAVIMFGVPYVYTQSRILKARLEYLRDQFQIRENDFLTFDAMRHA
AQCVGRAIRGKTDYGLMVFADKRFARGDKRGKLPRWIQEHLTDANLNLTVDEGVQVAKYF
LRQMAQPFHREDQLGLSLLSLEQLESEETLKRIEQIAQQLSSNDYKDDDDK

Sequence of entity 3 (C), FASTA

>28JM_3 General transcription factor IIH subunit 1 (chains C)
MATSSEEVLLIVKKVRQKKQDGALYLMAERIAWAPEGKDRFTISHMYADIKCQKISPEGK
AKIQLQLVLHAGDTTNFHFSNESTAVKERDAVKDLLQQLLPKFKRKANKELEEKNRMLQE
DPVLFQLYKDLVVSQVISAEEFWANRLNVNATDSSSTSNHKQDVGISAAFLADVRPQTDG
CNGLRYNLTSDIIESIFRTYPAVKMKYAENVPHNMTEKEFWTRFFQSHYFHRDRLNTGSK
DLFAECAKIDEKGLKTMVSLGVKNPLLDLTALEDKPLDEGYGISSVPSASNSKSIKENSN
AAIIKRFNHHSAMVLAAGLRKQEAQNEQTSEPSNMDGNSGDADCFQPAVKRAKLQESIEY
EDLGKNNSVKTIALNLKKSDRYYHGPTPIQSLQYATSQDIINSFQSIRQEMEAYTPKLTQ
VLSSSAASSTITALSPGGALMQGGTQQAINQMVPNDIQSELKHLYVAVGELLRHFWSCFP
VNTPFLEEKVVKMKSNLERFQVTKLCPFQEKIRRQYLSTNLVSHIEEMLQTAYNKLHTWQ
SRRLMKKTGSGGENLYFQSGSWSHPQFEKGGGSGGGSGGGSWSHPQFEKSG

Sequence of entity 4 (D), FASTA

>28JM_4 General transcription factor IIH subunit 4 (chains D)
MESTPSRGLNRVHLQCRNLQEFLGGLSPGVLDRLYGHPATCLAVFRELPSLAKNWVMRML
FLEQPLPQAAVALWVKKEFSKAQEESTGLLSGLRIWHTQLLPGGLQGLILNPIFRQNLRI
ALLGGGKAWSDDTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQLLS
QAGLMKSTEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQL
SFSTLGKDYSVEGMSDSLLNFLQHLREFGLVFQRKRKSRRYYPTRLAINLSSGVSGAGGT
VHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGIT
AQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFEL
LLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQKHSS

Sequence of entity 5 (E), FASTA

>28JM_5 General transcription factor IIH subunit 2 (chains E)
MDEEPERTKRWEGGYERTWEILKEDESGSLKATIEDILFKAKRKRVFEHHGQVRLGMMRH
LYVVVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTEL
SGNPRKHITSLKKAVDMTCHGEPSLYNSLSIAMQTLKHMPGHTSREVLIIFSSLTTCDPS
NIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETGGTYHVILDESHYKELLTHHVSPPP
ASSSSECSLIRMGFPQHTIASLSDQDAKPSFSMAHLDGNTEPGLTLGGYFCPQCRAKYCE
LPVECKICGLTLVSAPHLARSYHHLFPLDAFQEIPLEEYNGERFCYGCQGELKDQHVYVC
AVCQNVFCVDCDVFVHDSLHCCPGCIHKIPAPSGV

Sequence of entity 6 (F), FASTA

>28JM_6 General transcription factor IIH subunit 3 (chains F)
MVSDEDELNLLVIVVDANPIWWGKQALKESQFTLSKCIDAVMVLGNSHLFMNRSNKLAVI
ASHIQESRFLYPGKNGRLGDFFGDPGNPPEFNPSGSKDGKYELLTSANEVIVEEIKDLMT
KSDIKGQHTETLLAGSLAKALCYIHRMNKEVKDNQEMKSRILVIKAAEDSALQYMNFMNV
IFAAQKQNILIDACVLDSDSGLLQQACDITGGLYLKVPQMPSLLQYLLWVFLPDQDQRSQ
LILPPPVHVDYRAACFCHRNLIEIGYVCSVCLSIFCNFSPICTTCETAFKISLPPVLKAK
KKKLKVSA

Sequence of entity 7 (G), FASTA

>28JM_7 General transcription factor IIH subunit 5 (chains G)
MVNVLKGVLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGEL
MDQNAFSLTQK

Sequence of entity 8 (H), FASTA

>28JM_8 CDK-activating kinase assembly factor MAT1 (chains H)
MDDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRV
QLFEDPTVDKEVEIRKKVLKIYNKREEDFPSLREYNDFLEEVEEIVFNLTNNVDLDNTKK
KMEIYQKENKDVIQKNKLKLTREQEELEEALEVERQENEQRRLFIQKEEQLQQILKRKNK
QAFLDELESSDLPVALLLAQHKDRSTQLEMQLEKPKPVKPVTFSTGIKMGQHISLAPIHK
LEEALYEYQPLQIETYGPHVPELEMLGRLGYLNHVRAASPQDLAGGYTSSLACHRALQDA
FSGLFWQPS

Sequence of entity 9 (I), FASTA

>28JM_9 DNA repair protein complementing XP-C cells (chains I)
MARKRAAGGEPRGRELRSQKSKAKSKARREEEEEDAFEDEKPPKKSLLSKVSQGKRKRGC
SHPGGSADGPAKKKVAKVTVKSENLKVIKDEALSDGDDLRDFPSDLKKAHHLKRGATMNE
DSNEEEEESENDWEEVEELSEPVLGDVRESTAFSRSLLPVKPVEIEIETPEQAKTRERSE
KIKLEFETYLRRAMKRFNKGVHEDTHKVHLLCLLANGFYRNNICSQPDLHAIGLSIIPAR
FTRVLPRDVDTYYLSNLVKWFIGTFTVNAELSASEQDNLQTTLERRFAIYSARDDEELVH
IFLLILRALQLLTRLVLSLQPIPLKSATAKGKKPSKERLTADPGGSSETSSQVLENHTKP
KTSKGTKQEETFAKGTCRPSAKGKRNKGGRKKRSKPSSSEEDEGPGDKQEKATQRRPHGR
ERRVASRVSYKEESGSDEAGSGSDFELSSGEASDPSDEDSEPGPPKQRKAPAPQRTKAGS
KSASRTHRGSHRKDPSLPAASSSSSSSKRGKKMCSDGEKAEKRSIAGIDQWLEVFCEQEE
KWVCVDCVHGVVGQPLTCYKYATKPMTYVVGIDSDGWVRDVTQRYDPVWMTVTRKCRVDA
EWWAETLRPYQSPFMDREKKEDLEFQAKHMDQPLPTAIGLYKNHPLYALKRHLLKYEAIY
PETAAILGYCRGEAVYSRDCVHTLHSRDTWLKKARVVRLGEVPYKMVKGFSNRARKARLA
EPQLREENDLGLFGYWQTEEYQPPVAVDGKVPRNEFGNVYLFLPSMMPIGCVQLNLPNLH
RVARKLDIDCVQAITGFDFHGGYSHPVTDGYIVCEEFKDVLLTAWENEQAVIERKEKEKK
EKRALGNWKLLAKGLLIRERLKRRYGPKSEAAAPHTDAGGGLSSDEEEGTSSQAEAARIL
AASWPQNREDEEKQKLKGGPKKTKREKKAAASHLFPFEQL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	7
SF4	Iron/sulfur cluster	Fe4 S4	1

Primary citation

Visualization of stepwise derepression of TFIIH in global genome nucleotide excision repair. de Martin Garrido, N., Haste, C.A.F., Feng, J. et al. Sci Adv (2026) 12:eaeb3506-eaeb3506. DOI 10.1126/sciadv.aeb3506 · 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)
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
8EBX 3.6 Å, XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (AP)

Browse structure collections

About this viewer

MolViewer shows 28JM directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.