8EBX: PDB entry 8EBX

XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (AP). Determined by electron microscopy at 3.6 Å resolution. Released 19 Apr 2023.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Homo sapiens, synthetic construct
Chains: 12
Atoms: 27,533
Mol. weight: 565 kDa
Ligands: CA, ZN, SF4
Released: 19 Apr 2023

Explore 8EBX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8EBX contains 166 α-helices and 134 β-strands across 10 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, 28 β-strands

Element	Residues	Length	Sheet
β-strand	59-60	2	1
β-strand	76-78	3	2
β-strand	84-87	4	2
α-helix	93-101	9
β-strand	105-108	4	2
β-strand	113-117	5	2
α-helix	120-128	9
α-helix	133-142	10
α-helix	152-161	10
β-strand	166-171	6	3
β-strand	174-179	6	3
α-helix	183-189	7
α-helix	192-195	4
β-strand	268-271	4	3
α-helix	274-276	3
α-helix	277-286	10
β-strand	294-295	2	4
α-helix	318-327	10
β-strand	328	1	4
β-strand	330	1	5
β-strand	333-334	2	4
β-strand	336-339	4	6
α-helix	347-357	11
β-strand	361-365	5	6
α-helix	370-381	12
β-strand	390-392	3	6
β-strand	405-409	5	6
α-helix	421-430	10
β-strand	435	1	7
β-strand	438-441	4	6
α-helix	443-445	3
α-helix	451-457	7
β-strand	460	1	7
β-strand	463-467	5	6
α-helix	477-483	7
β-strand	487-490	4	6
α-helix	493-498	6
β-strand	505-512	8	8
α-helix	513-515	3
α-helix	516-524	9
α-helix	531-535	5
α-helix	538-553	16
β-strand	558-562	5	8
α-helix	565-573	9
β-strand	579-580	2	8
α-helix	587-597	11
β-strand	604-607	4	8
β-strand	622-626	5	8
α-helix	633-641	9
β-strand	657-664	8	8
α-helix	668-676	9
α-helix	678-683	6
β-strand	688-690	3	8
α-helix	706-717	12

Chain B: 34 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	9
β-strand	8-11	4	9
α-helix	19-34	16
β-strand	38-41	4	10
α-helix	48-62	15
β-strand	70-71	2	11
β-strand	74	1	12
α-helix	77-98	22
β-strand	106-108	3	11
α-helix	127-137	11
α-helix	140-145	6
α-helix	146-148	3
α-helix	157-164	8
α-helix	177-187	11
α-helix	191-198	8
β-strand	204-206	3	11
β-strand	208	1	12
α-helix	210-213	4
α-helix	215-221	7
β-strand	230-231	2	11
β-strand	232-234	3	10
α-helix	239-246	8
β-strand	250-251	2	13
α-helix	253-271	19
α-helix	327-334	8
α-helix	336-345	10
α-helix	356-364	9
α-helix	370-379	10
α-helix	382-386	5
α-helix	395-409	15
β-strand	414	1	14
β-strand	417-419	3	13
β-strand	432-434	3	13
β-strand	437	1	14
α-helix	445-448	4
β-strand	455-458	4	10
α-helix	467-470	4
β-strand	490-495	6	15
α-helix	508-510	3
α-helix	514-528	15
β-strand	535-539	5	15
α-helix	542-554	13
α-helix	558-562	5
β-strand	566-569	4	15
α-helix	574-589	16
β-strand	594-599	6	15
α-helix	603-607	5
β-strand	617-620	4	15
α-helix	633-643	11
α-helix	648-664	17
α-helix	665-667	3
β-strand	675-680	6	15
α-helix	682-685	4
α-helix	687-690	4
α-helix	695-698	4
β-strand	708	1	15
α-helix	710-724	15

Chain C: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	112-120	9
α-helix	122-128	7
α-helix	129-133	5
α-helix	139-146	8
α-helix	399-412	14
α-helix	419-421	3
α-helix	424-434	11
α-helix	455-478	24
α-helix	484-500	17
α-helix	501-505	5
α-helix	506-515	10
α-helix	521-546	26

Chain D: 25 helices, 18 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
α-helix	59-61	3
β-strand	66-67	2	16
α-helix	68-72	5
β-strand	75	1	17
α-helix	80-93	14
β-strand	96-100	5	16
β-strand	106-110	5	16
α-helix	112-122	11
α-helix	145-164	20
α-helix	173-182	10
β-strand	185-186	2	18
α-helix	193-194	2
β-strand	195-196	2	18
α-helix	198-205	8
α-helix	208-221	14
α-helix	223-226	4
α-helix	230-241	12
α-helix	244	1
β-strand	249-250	2	19
α-helix	256-268	13
β-strand	271-272	2	20
β-strand	280-281	2	19
β-strand	282-283	2	20
α-helix	285-288	4
β-strand	307-310	4	1
β-strand	314-317	4	1
α-helix	322-330	9
β-strand	333-338	6	1
β-strand	341-345	5	1
α-helix	348-356	9
α-helix	361-370	10
β-strand	372	1	1
α-helix	374-378	5
α-helix	385-398	14
β-strand	402-409	8	21
α-helix	415-428	14
β-strand	431-435	5	21
β-strand	440-443	4	21
α-helix	448-461	14

Chain E: 21 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	5
α-helix	15-16	2
α-helix	18-20	3
α-helix	30-41	12
β-strand	59-66	8	22
α-helix	69-72	4
α-helix	80-98	19
β-strand	103-110	8	22
β-strand	113-121	9	22
α-helix	124-133	10
α-helix	134-136	3
α-helix	145-156	12
β-strand	164-170	7	22
α-helix	182-191	10
β-strand	195-200	6	22
α-helix	206-215	10
β-strand	219-221	3	22
α-helix	225-236	12
α-helix	238-240	3
β-strand	251-253	3	23
β-strand	257-258	2	24
α-helix	273-276	4
α-helix	281-282	2
β-strand	288-290	3	24
β-strand	297-298	2	24
β-strand	303-304	2	23
α-helix	310	1
β-strand	311-312	2	23
α-helix	315-319	5
α-helix	322-325	4
α-helix	327-331	5
β-strand	332-335	4	25
β-strand	344	1	26
β-strand	351	1	26
β-strand	356-359	4	25
β-strand	366-367	2	25
α-helix	369-374	6
α-helix	375-379	5
α-helix	383-386	4

Chain F: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7-16	10	27
α-helix	19-27	9
α-helix	34-51	18
β-strand	56-62	7	27
β-strand	67-69	3	27
α-helix	102-120	19
α-helix	133-150	18
β-strand	156-165	10	27
α-helix	174-186	13
β-strand	190-195	6	27
α-helix	201-210	10
β-strand	214-216	3	27
α-helix	220-222	3
α-helix	223-226	4
α-helix	227-231	5
α-helix	235-240	6
β-strand	241	1	17
α-helix	244-247	4
β-strand	253-254	2	28
β-strand	261-262	2	28
β-strand	264-267	4	23
β-strand	274-275	2	23
α-helix	283-287	5

Chain G: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	21
α-helix	14-26	13
β-strand	34-39	6	21
β-strand	42-45	4	21
α-helix	47-49	3
α-helix	50-63	14

Chain H: 18 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	638-641	4
β-strand	647-648	2	29
β-strand	658-659	2	30
α-helix	664-666	3
β-strand	668-670	3	31
β-strand	673-675	3	31
β-strand	676-677	2	29
β-strand	681-682	2	30
β-strand	685-686	2	32
α-helix	687-692	6
β-strand	695-697	3	33
α-helix	698	1
α-helix	701-703	3
β-strand	705-707	3	32
α-helix	712-720	9
α-helix	722-724	3
β-strand	730-733	4	32
α-helix	735-737	3
β-strand	738-740	3	33
β-strand	745	1	34
β-strand	747	1	35
β-strand	750	1	35
β-strand	759-760	2	36
α-helix	764-766	3
α-helix	768	1
β-strand	769	1	34
β-strand	771-774	4	36
α-helix	779-786	8
β-strand	791-798	8	36
α-helix	800-802	3
β-strand	805-814	10	36
α-helix	818-864	47
α-helix	890-901	12
α-helix	909-914	6
α-helix	920-921	2
α-helix	925-933	9
α-helix	936-938	3

2 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
TFIIH basal transcription factor complex helicase XPB subunit	A	protein	782	Homo sapiens	P19447 (AlphaFold model)
General transcription and DNA repair factor IIH helicase subunit XPD	B	protein	768	Homo sapiens	P18074 (AlphaFold model)
General transcription factor IIH subunit 1	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	E	protein	417	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
Xeroderma pigmentosum, complementation group C, isoform CRA_a	H	protein	950	Homo sapiens	Q01831
Centrin-2	J	protein	172	Homo sapiens	P41208
DNA repair protein complementing XP-A cells	K	protein	273	Homo sapiens	P23025
DNA (Ap)	L	DNA	40	synthetic construct
DNA	M	DNA	40	synthetic construct

Sequence of entity 1 (A), FASTA

>8EBX_1 TFIIH basal transcription factor complex helicase XPB subunit (chains A)
MGKRDRADRDKKKSRKRHYEDEEDDEEDAPGNDPQEAVPSAAGKQVDESGTKVDEYGAKD
YRLQMPLKDDHTSRPLWVAPDGHIFLEAFSPVYKYAQDFLVAIAEPVCRPTHVHEYKLTA
YSLYAAVSVGLQTSDITEYLRKLSKTGVPDGIMQFIKLCTVSYGKVKLVLKHNRYFVESC
HPDVIQHLLQDPVIRECRLRNSEGEATELITETFTSKSAISKTAESSGGPSTSRVTDPQG
KSDIPMDLFDFYEQMDKDEEEEEETQTVSFEVKQEMIEELQKRCIHLEYPLLAEYDFRND
SVNPDINIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKR
CLVLGNSAVSVEQWKAQFKMWSTIDDSQICRFTSDAKDKPIGCSVAISTYSMLGHTTKRS
WEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLTATLVREDDKIVDL
NFLIGPKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNK
FRACQFLIKFHERRNDKIIVFADNVFALKEYAIRLNKPYIYGPTSQGERMQILQNFKHNP
KINTIFISKVGDTSFDLPEANVLIQISSHGGSRRQEAQRLGRVLRAKKGMVAEEYNAFFY
SLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEEDLAFSTKEEQQQLLQKVLAAT
DLDAEEEVVAGEFGSRSSQASRRFGTMSSMSGADDTVYMEYHSSRSKAPSKHVHPLFKRF
RK

Sequence of entity 2 (B), FASTA

>8EBX_2 General transcription and DNA repair factor IIH helicase subunit XPD (chains B)
MKLNVDGLLVYFPYDYIYPEQFSYMRELKRTLDAKGHGVLEMPSGTGKTVSLLALIMAYQ
RAYPLEVTKLIYCSRTVPEIEKVIEELRKLLNFYEKQEGEKLPFLGLALSSRKNLCIHPE
VTPLRFGKDVDGKCHSLTASYVRAQYQHDTSLPHCRFYEEFDAHGREVPLPAGIYNLDDL
KALGRRQGWCPYFLARYSILHANVVVYSYHYLLDPKIADLVSKELARKAVVVFDEAHNID
NVCIDSMSVNLTRRTLDRCQGNLETLQKTVLRIKETDEQRLRDEYRRLVEGLREASAARE
TDAHLANPVLPDEVLQEAVPGSIRTAEHFLGFLRRLLEYVKWRLRVQHVVQESPPAFLSG
LAQRVCIQRKPLRFCAERLRSLLHTLEITDLADFSPLTLLANFATLVSTYAKGFTIIIEP
FDDRTPTIANPILHFSCMDASLAIKPVFERFQSVIITSGTLSPLDIYPKILDFHPVTMAT
FTMTLARVCLCPMIIGRGNDQVAISSKFETREDIAVIRNYGNLLLEMSAVVPDGIVAFFT
SYQYMESTVASWYEQGILENIQRNKLLFIETQDGAETSVALEKYQEACENGRGAILLSVA
RGKVSEGIDFVHHYGRAVIMFGVPYVYTQSRILKARLEYLRDQFQIRENDFLTFDAMRHA
AQCVGRAIRGKTDYGLMVFADKRFARGDKRGKLPRWIQEHLTDANLNLTVDEGVQVAKYF
LRQMAQPFHREDQLGLSLLSLEQLESEETLKRIEQIAQQLDYKDDDDK

Sequence of entity 3 (C), FASTA

>8EBX_3 General transcription factor IIH subunit 1 (chains C)
MATSSEEVLLIVKKVRQKKQDGALYLMAERIAWAPEGKDRFTISHMYADIKCQKISPEGK
AKIQLQLVLHAGDTTNFHFSNESTAVKERDAVKDLLQQLLPKFKRKANKELEEKNRMLQE
DPVLFQLYKDLVVSQVISAEEFWANRLNVNATDSSSTSNHKQDVGISAAFLADVRPQTDG
CNGLRYNLTSDIIESIFRTYPAVKMKYAENVPHNMTEKEFWTRFFQSHYFHRDRLNTGSK
DLFAECAKIDEKGLKTMVSLGVKNPLLDLTALEDKPLDEGYGISSVPSASNSKSIKENSN
AAIIKRFNHHSAMVLAAGLRKQEAQNEQTSEPSNMDGNSGDADCFQPAVKRAKLQESIEY
EDLGKNNSVKTIALNLKKSDRYYHGPTPIQSLQYATSQDIINSFQSIRQEMEAYTPKLTQ
VLSSSAASSTITALSPGGALMQGGTQQAINQMVPNDIQSELKHLYVAVGELLRHFWSCFP
VNTPFLEEKVVKMKSNLERFQVTKLCPFQEKIRRQYLSTNLVSHIEEMLQTAYNKLHTWQ
SRRLMKKT

Sequence of entity 4 (D), FASTA

>8EBX_4 General transcription factor IIH subunit 4,  p52 (chains D)
MESTPSRGLNRVHLQCRNLQEFLGGLSPGVLDRLYGHPATCLAVFRELPSLAKNWVMRML
FLEQPLPQAAVALWVKKEFSKAQEESTGLLSGLRIWHTQLLPGGLQGLILNPIFRQNLRI
ALLGGGKAWSDDTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQLLS
QAGLMKSTEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQL
SFSTLGKDYSVEGMSDSLLNFLQHLREFGLVFQRKRKSRRYYPTRLAINLSSGVSGAGGT
VHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGIT
AQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFEL
LLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQKHSS

Sequence of entity 5 (E), FASTA

>8EBX_5 General transcription factor IIH subunit 2 (chains E)
MGSSHHHHHHSSGLEVLFQGPHMDEEPERTKRWEGGYERTWEILKEDESGSLKATIEDIL
FKAKRKRVFEHHGQVRLGMMRHLYVVVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQ
NPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKKAVDMTCHGEPSLYNSLSIAMQTLKH
MPGHTSREVLIIFSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETGGT
YHVILDESHYKELLTHHVSPPPASSSSECSLIRMGFPQHTIASLSDQDAKPSFSMAHLDG
NTEPGLTLGGYFCPQCRAKYCELPVECKICGLTLVSAPHLARSYHHLFPLDAFQEIPLEE
YNGERFCYGCQGELKDQHVYVCAVCQNVFCVDCDVFVHDSLHCCPGCIHKIPAPSGV

Sequence of entity 6 (F), FASTA

>8EBX_6 General transcription factor IIH subunit 3 (chains F)
MVSDEDELNLLVIVVDANPIWWGKQALKESQFTLSKCIDAVMVLGNSHLFMNRSNKLAVI
ASHIQESRFLYPGKNGRLGDFFGDPGNPPEFNPSGSKDGKYELLTSANEVIVEEIKDLMT
KSDIKGQHTETLLAGSLAKALCYIHRMNKEVKDNQEMKSRILVIKAAEDSALQYMNFMNV
IFAAQKQNILIDACVLDSDSGLLQQACDITGGLYLKVPQMPSLLQYLLWVFLPDQDQRSQ
LILPPPVHVDYRAACFCHRNLIEIGYVCSVCLSIFCNFSPICTTCETAFKISLPPVLKAK
KKKLKVSA

Sequence of entity 7 (G), FASTA

>8EBX_7 General transcription factor IIH subunit 5 (chains G)
MVNVLKGVLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGEL
MDQNAFSLTQK

Sequence of entity 8 (H), FASTA

>8EBX_8 Xeroderma pigmentosum, complementation group C, isoform CRA_a (chains H)
MDYKDDDDKHMARKRAAGGEPRGRELRSQKSKAKSKARREEEEEDAFEDEKPPKKSLLSK
VSQGKRKRGCSHPGGSADGPAKKKVAKVTVKSENLKVIKDEALSDGDDLRDFPSDLKKAH
HLKRGATMNEDSNEEEEESENDWEEVEELSEPVLGDVRESTAFSRSLLPVKPVEIEIETP
EQAKTRERSEKIKLEFETYLRRAMKRFNKGVHEDTHKVHLLCLLANGFYRNNICSQPDLH
AIGLSIIPARFTRVLPRDVDTYYLSNLVKWFIGTFTVNAELSASEQDNLQTTLERRFAIY
SARDDEELVHIFLLILRALQLLTRLVLSLQPIPLKSATAKGKKPSKERLTADPGGSSETS
SQVLENHTKPKTSKGTKQEETFAKGTCRPSAKGKRNKGGRKKRSKPSSSEEDEGPGDKQE
KATQRRPHGRERRVASRVSYKEESGSDEAGSGSDFELSSGEASDPSDEDSEPGPPKQRKA
PAPQRTKAGSKSASRTHRGSHRKDPSLPVASSSSSSSKRGKKMCSDGEKAEKRSIAGIDQ
WLEVFCEQEEKWVCVDCVHGVVGQPLTCYKYATKPMTYVVGIDSDGWVRDVTQRYDPVWM
TVTRKCRVDAEWWAETLRPYQSPFMDREKKEDLEFQAKHMDQPLPTAIGLYKNHPLYALK
RHLLKYEAIYPETAAILGYCRGEAVYSRDCVHTLHSRDTWLKKARVVRLGEVPYKMVKGF
SNRARKARLAEPQLREENDLGLFGYWQTEEYQPPVAVDGKVPRNEFGNVYLFLPSMMPIG
CVQLNLPNLHRVARKLDIDCVQAITGFDFHGGYSHPVTDGYIVCEEFKDVLLTAWENEQA
VIERKEKEKKEKRALGNWKLLAKGLLIRERLKRRYGPKSEAAAPHTDAGGGLSSDEEEGT
SSQAEAARILAASWPQNREDEEKQKLKGGPKKTKREKKAAASHLFPFEKL

Sequence of entity 9 (J), FASTA

>8EBX_9 Centrin-2 (chains J)
MASNFKKANMASSSQRKRMSPKPELTEEQKQEIREAFDLFDADGTGTIDVKELKVAMRAL
GFEPKKEEIKKMISEIDKEGTGKMNFGDFLTVMTQKMSEKDTKEEILKAFKLFDDDETGK
ISFKNLKRVAKELGENLTDEELQEMIDEADRDGDGEVSEQEFLRIMKKTSLY

Sequence of entity 10 (K), FASTA

>8EBX_10 DNA repair protein complementing XP-A cells (chains K)
MAAADGALPEAAALEQPAELPASVRASIERKRQRALMLRQARLAARPYSATAAAATGGMA
NVKAAPKIIDTGGGFILEEEEEEEQKIGKVVHQPGPVMEFDYVICEECGKEFMDSYLMNH
FDLPTCDNCRDADDKHKLITKTEAKQEYLLKDCDLEKREPPLKFIVKKNPHHSQWGDMKL
YLKLQIVKRSLEVWGSQEALEEAKEVRQENREKMKQKKFDKKVKELRRAVRSSVWKRETI
VHQHEYGPEENLEDDMYRKTCTMCGHELTYEKM

Sequence of entity 11 (L), FASTA

>8EBX_11 DNA (Ap) (chains L)
AGGTAGTCACAGCTGATTGCGCTGAGGATNNTAGACGTGC

Sequence of entity 12 (M), FASTA

>8EBX_12 DNA (chains M)
GCACGTCTATTATCCTCAGCGCAATCAGCTGTGACTACCT

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
ZN	Zinc ion	Zn	6
SF4	Iron/sulfur cluster	Fe4 S4	1

Primary citation

Lesion recognition by XPC, TFIIH and XPA in DNA excision repair. Kim, J., Li, C.L., Chen, X. et al. Nature (2023) 617:170-175. DOI 10.1038/s41586-023-05959-z · 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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