7NVV: General transcription factor IIH subunit 4

Name: PDB 7NVV: XPB-containing part of TFIIH in a post-translocated state (with ADP-BeF3)
Published: 2021-05-05
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

XPB-containing part of TFIIH in a post-translocated state (with ADP-BeF3). Determined by electron microscopy at 2.9 Å resolution. Released 5 May 2021.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Homo sapiens, Human mastadenovirus C
Chains: 8
Atoms: 9,071
Mol. weight: 267.24 kDa
Ligands: ADP, BEF, MG
Released: 5 May 2021

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

Secondary structure: helices and β-sheets

7NVV contains 57 α-helices and 54 β-strands across 5 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 2: 17 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	146-163	18
α-helix	173-179	7
α-helix	180-184	5
β-strand	185-186	2	1
α-helix	193-194	2
β-strand	195-196	2	1
α-helix	198-205	8
α-helix	208-226	19
α-helix	230-241	12
α-helix	256-267	12
β-strand	271-272	2	2
β-strand	282-283	2	2
α-helix	285-288	4
β-strand	307-309	3	3
β-strand	314-317	4	3
α-helix	322-330	9
β-strand	333-338	6	3
β-strand	341-345	5	3
α-helix	348-357	10
α-helix	361-370	10
β-strand	372	1	3
α-helix	374-378	5
α-helix	385-398	14
β-strand	402-409	8	4
α-helix	415-428	14
β-strand	431-435	5	4
β-strand	440-443	4	4
α-helix	445-447	3
α-helix	448-457	10

Chain 5: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	4-11	8	4
α-helix	14-26	13
β-strand	34-37	4	4
β-strand	42-45	4	4
α-helix	47-49	3
α-helix	50-63	14

Chain 7: 35 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	53	1	3
β-strand	59-60	2	3
β-strand	76-78	3	5
β-strand	83-87	5	5
α-helix	93-103	11
β-strand	105-108	4	5
β-strand	113-117	5	5
α-helix	120-129	10
α-helix	133-143	11
β-strand	144	1	5
α-helix	150-158	9
β-strand	166-171	6	6
β-strand	174-179	6	6
α-helix	182-190	9
α-helix	192-196	5
β-strand	198	1	6
β-strand	267	1	7
β-strand	268-272	5	6
α-helix	274-276	3
α-helix	277-286	10
β-strand	291-292	2	6
β-strand	294-295	2	8
α-helix	297-299	3
α-helix	304-306	3
β-strand	310	1	9
α-helix	318-327	10
β-strand	333-334	2	8
α-helix	335	1
β-strand	336-339	4	10
α-helix	346-357	12
β-strand	361-365	5	10
α-helix	368-381	14
β-strand	382	1	9
β-strand	389-392	4	10
β-strand	397	1	10
β-strand	405-409	5	10
α-helix	410-414	5
α-helix	418-420	3
α-helix	421-431	11
β-strand	434-435	2	11
β-strand	437-441	5	10
α-helix	443-445	3
α-helix	453-457	5
β-strand	459-460	2	11
β-strand	463-467	5	10
α-helix	477-479	3
α-helix	480-483	4
β-strand	487-490	4	10
α-helix	493-499	7
β-strand	502	1	12
β-strand	505-510	6	13
β-strand	511-512	2	14
α-helix	513-515	3
α-helix	516-524	9
α-helix	530-535	6
α-helix	538-552	15
β-strand	558-561	4	13
α-helix	565-575	11
β-strand	579-580	2	13
α-helix	586-598	13
β-strand	604-607	4	13
α-helix	609-612	4
β-strand	622-625	4	13
α-helix	633-640	8
α-helix	641-643	3
β-strand	645	1	12
α-helix	646-647	2
β-strand	657-661	5	13
β-strand	663-664	2	14
α-helix	668-676	9
α-helix	678-682	5
β-strand	688-690	3	13
α-helix	706-719	14

Chain W: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	276-278	3
α-helix	279-282	4

Chain Y: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	7	1	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
General transcription factor IIH subunit 4	2	protein	462	Homo sapiens	Q92759 (AlphaFold model)
General transcription factor IIH subunit 5	5	protein	71	Homo sapiens	Q6ZYL4 (AlphaFold model)
General transcription and DNA repair factor IIH helicase subunit XPB	7	protein	782	Homo sapiens	P19447 (AlphaFold model)
Non-template DNA	N	DNA	106	Human mastadenovirus C
Template DNA	T	DNA	106	Human mastadenovirus C
General transcription factor IIE subunit 1	W	protein	439	Homo sapiens	P29083 (AlphaFold model)
Unassigned peptide, likely XPB	Y	protein	8	Homo sapiens
Unassigned Peptide, likely TFIIE-Beta	Z	protein	16	Homo sapiens

Sequence of entity 1 (2), FASTA

>7NVV_1 General transcription factor IIH subunit 4 (chains 2)
MESTPSRGLNRVHLQCRNLQEFLGGLSPGVLDRLYGHPATCLAVFRELPSLAKNWVMRML
FLEQPLPQAAVALWVKKEFSKAQEESTGLLSGLRIWHTQLLPGGLQGLILNPIFRQNLRI
ALLGGGKAWSDDTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQLLS
QAGLMKSTEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQL
SFSTLGKDYSVEGMSDSLLNFLQHLREFGLVFQRKRKSRRYYPTRLAINLSSGVSGAGGT
VHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGIT
AQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFEL
LLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQKHSS

Sequence of entity 2 (5), FASTA

>7NVV_2 General transcription factor IIH subunit 5 (chains 5)
MVNVLKGVLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGEL
MDQNAFSLTQK

Sequence of entity 3 (7), FASTA

>7NVV_3 General transcription and DNA repair factor IIH helicase subunit XPB (chains 7)
MGKRDRADRDKKKSRKRHYEDEEDDEEDAPGNDPQEAVPSAAGKQVDESGTKVDEYGAKD
YRLQMPLKDDHTSRPLWVAPDGHIFLEAFSPVYKYAQDFLVAIAEPVCRPTHVHEYKLTA
YSLYAAVSVGLQTSDITEYLRKLSKTGVPDGIMQFIKLCTVSYGKVKLVLKHNRYFVESC
HPDVIQHLLQDPVIRECRLRNSEGEATELITETFTSKSAISKTAESSGGPSTSRVTDPQG
KSDIPMDLFDFYEQMDKDEEEEEETQTVSFEVKQEMIEELQKRCIHLEYPLLAEYDFRND
SVNPDINIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKR
CLVLGNSAVSVEQWKAQFKMWSTIDDSQICRFTSDAKDKPIGCSVAISTYSMLGHTTKRS
WEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLTATLVREDDKIVDL
NFLIGPKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNK
FRACQFLIKFHERRNDKIIVFADNVFALKEYAIRLNKPYIYGPTSQGERMQILQNFKHNP
KINTIFISKVGDTSFDLPEANVLIQISSHGGSRRQEAQRLGRVLRAKKGMVAEEYNAFFY
SLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEEDLAFSTKEEQQQLLQKVLAAT
DLDAEEEVVAGEFGSRSSQASRRFGTMSSMSGADDTVYMEYHSSRSKAPSKHVHPLFKRF
RK

Sequence of entity 4 (N), FASTA

>7NVV_4 Non-template DNA (chains N)
CGGGTGTTCCTGAAGGGGGGCTATAAAAGGGGGTGGGGGCGCGTTCGTCCTCACTCTCTT
CCGCATCGCTGTCTGCGAGGGCCAGCTGTTGGGGTGAGTACTCCCT

Sequence of entity 5 (T), FASTA

>7NVV_5 Template DNA (chains T)
AGGGAGTACTCACCCCAACAGCTGGCCCTCGCAGACAGCGATGCGGAAGAGAGTGAGGAC
GAACGCGCCCCCACCCCCTTTTATAGCCCCCCTTCAGGAACACCCG

Sequence of entity 6 (W), FASTA

>7NVV_6 General transcription factor IIE subunit 1 (chains W)
MADPDVLTEVPAALKRLAKYVIRGFYGIEHALALDILIRNSCVKEEDMLELLKFDRKQLR
SVLNNLKGDKFIKCRMRVETAADGKTTRHNYYFINYRTLVNVVKYKLDHMRRRIETDERD
STNRASFKCPVCSSTFTDLEANQLFDPMTGTFRCTFCHTEVEEDESAMPKKDARTLLARF
NEQIEPIYALLRETEDVNLAYEILEPEPTEIPALKQSKDHAATTAGAASLAGGHHREAWA
TKGPSYEDLYTQNVVINMDDQEDLHRASLEGKSAKERPIWLRESTVQGAYGSEDMKEGGI
DMDAFQEREEGHAGPDDNEEVMRALLIHEKKTSSAMAGSVGAAAPVTAANGSDSESETSE
SDDDSPPRPAAVAVHKREEDEEEDDEFEEVADDPIVMVAGRPFSYSEVSQRPELVAQMTP
EEKEAYIAMGQRMFEDLFE

Sequence of entity 7 (Y), FASTA

>7NVV_7 Unassigned peptide, likely XPB (chains Y)
XXXXXXXX

Sequence of entity 8 (Z), FASTA

>7NVV_8 Unassigned Peptide, likely TFIIE-Beta (chains Z)
XXXXXXXXXXXXXXXX

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
BEF	Beryllium trifluoride ion	Be F3	1
MG	Magnesium ion	Mg	1

Primary citation

Structures of mammalian RNA polymerase II pre-initiation complexes. Aibara, S., Schilbach, S., Cramer, P. Nature (2021) 594:124-128. DOI 10.1038/s41586-021-03554-8 · PubMed

Other PDB entries of the same protein (UniProt Q92759 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
8EBX 3.6 Å, XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (AP)
8EBY 3.6 Å, XPC release from Core7-XPA-DNA (AP)

Browse structure collections

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