8UOT: Composite map of PICdeltaTFIIK form1

Name: PDB 8UOT: Composite map of PICdeltaTFIIK form1
Published: 2024-10-23
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Composite map of PICdeltaTFIIK form1. Determined by electron microscopy at 3.7 Å resolution. Released 23 Oct 2024.

Method: Electron microscopy
Resolution: 3.7 Å
Organism: Saccharomyces cerevisiae
Chains: 30
Atoms: 70,523
Mol. weight: 1336.83 kDa
Ligands: SF4, ZN, MG
Released: 23 Oct 2024

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

Secondary structure: helices and β-sheets

8UOT contains 377 α-helices and 410 β-strands across 28 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 0: 41 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
β-strand	9-11	3	1
β-strand	17	1	2
α-helix	19-34	16
β-strand	39-41	3	3
α-helix	49-62	14
β-strand	69-73	5	3
α-helix	76-97	22
α-helix	100-102	3
β-strand	104-106	3	3
α-helix	111-114	4
α-helix	118-121	4
α-helix	126-137	12
α-helix	140-147	8
α-helix	157-164	8
β-strand	174-175	2	3
α-helix	178-188	11
α-helix	192-199	8
β-strand	205-209	5	3
α-helix	211-214	4
α-helix	220-224	5
β-strand	231-235	5	3
α-helix	240-247	8
β-strand	250-252	3	4
α-helix	254-277	24
α-helix	280-291	12
α-helix	295-298	4
α-helix	313-315	3
α-helix	320-322	3
α-helix	323-326	4
α-helix	328-346	19
β-strand	352-354	3	4
α-helix	356-366	11
α-helix	371-388	18
α-helix	394-396	3
α-helix	397-409	13
β-strand	416-421	6	4
β-strand	434-439	6	4
α-helix	446-452	7
β-strand	456-460	5	3
α-helix	468-472	5
β-strand	480-482	3	3
β-strand	492-494	3	5
β-strand	497	1	6
α-helix	516-532	17
β-strand	536-541	6	5
α-helix	544-557	14
α-helix	559-564	6
β-strand	568-571	4	5
α-helix	576-592	17
β-strand	596-601	6	5
α-helix	605-607	3
β-strand	619-622	4	5
α-helix	627-629	3
α-helix	633-646	14
α-helix	650-666	17
β-strand	677-679	3	5
α-helix	684-689	6
α-helix	695-700	6
α-helix	704-706	3
β-strand	708	1	6
α-helix	710-724	15
α-helix	730-732	3
β-strand	739	1	2
α-helix	741-751	11

Chain 1: 28 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	171-176	6
α-helix	178-187	10
α-helix	190-195	6
α-helix	196-201	6
α-helix	206-212	7
α-helix	214-225	12
α-helix	228-230	3
α-helix	233-236	4
α-helix	253-262	10
α-helix	264-271	8
α-helix	280-289	10
α-helix	291-296	6
α-helix	309-312	4
α-helix	315-329	15
α-helix	339-343	5
α-helix	353-355	3
α-helix	371-389	19
α-helix	414-418	5
α-helix	422-424	3
α-helix	426-428	3
β-strand	432	1	10
α-helix	433	1
β-strand	434	1	11
α-helix	441-443	3
α-helix	466-482	17
α-helix	487-489	3
α-helix	495-514	20
α-helix	544-570	27
α-helix	576-604	29
α-helix	609-637	29

Chain 2: 22 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	6-16	11
α-helix	19-25	7
α-helix	29-38	10
α-helix	41-50	10
β-strand	57-58	2	13
α-helix	59-65	7
α-helix	68-70	3
α-helix	71-83	13
β-strand	87	1	14
β-strand	90-92	3	13
β-strand	95-98	4	13
β-strand	100	1	14
α-helix	102-113	12
β-strand	124	1	15
α-helix	135-151	17
α-helix	161-169	9
β-strand	174-176	3	16
β-strand	181-183	3	16
α-helix	186-193	8
α-helix	196-210	15
α-helix	218-230	13
β-strand	237	1	15
α-helix	244-255	12
β-strand	259-261	3	17
β-strand	269-271	3	17
α-helix	273-279	7
β-strand	339-340	2	18
β-strand	346-350	5	18
α-helix	354-360	7
β-strand	365-369	5	18
β-strand	373-377	5	18
α-helix	380-388	9
α-helix	393-401	9
α-helix	406-422	17
α-helix	438-449	12
β-strand	452-453	2	12
β-strand	459	1	19
α-helix	465-477	13
β-strand	481-485	5	19
β-strand	490-493	4	19
α-helix	498-506	9

Chain 4: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	24-31	8	20
α-helix	34-43	10
α-helix	49-67	19
β-strand	73-79	7	20
β-strand	82-87	6	20
α-helix	116-138	23
α-helix	149-165	17
β-strand	173-181	9	20
α-helix	190-206	17
β-strand	210-215	6	20
α-helix	222-230	9
β-strand	235-238	4	20
α-helix	244-250	7
β-strand	275	1	21
β-strand	282	1	21
β-strand	285-289	5	22
β-strand	295-296	2	22
α-helix	299-300	2
α-helix	301-303	3
β-strand	304	1	23
β-strand	311	1	23
α-helix	314-320	7
α-helix	322-325	4

Chain 5: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	12
α-helix	14-26	13
β-strand	31-36	6	12
β-strand	39-42	4	12
α-helix	44-46	3
α-helix	47-61	15

Chain 6: 15 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	97-109	13
β-strand	118	1	11
β-strand	120	1	24
β-strand	124-131	8	25
α-helix	135-137	3
α-helix	145-163	19
β-strand	168-175	8	25
β-strand	178-183	6	25
α-helix	189-201	13
α-helix	210-221	12
β-strand	229-236	8	25
α-helix	248-256	9
β-strand	260-265	6	25
α-helix	271-280	10
β-strand	288-290	3	25
α-helix	294-305	12
β-strand	309	1	24
β-strand	311	1	10
β-strand	319-323	5	22
β-strand	326-327	2	26
β-strand	334-335	2	27
β-strand	342-343	2	27
β-strand	347-348	2	26
β-strand	355	1	26
β-strand	361-362	2	22
β-strand	369-370	2	22
α-helix	373-377	5
α-helix	380-383	4
β-strand	390-391	2	28
α-helix	392-393	2
β-strand	402	1	29
β-strand	409	1	29
α-helix	410-411	2
β-strand	427-429	3	28
β-strand	434-436	3	28
α-helix	438-442	5
α-helix	443-447	5
α-helix	452-456	5

Chain 7: 28 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	105-107	3
α-helix	125-127	3
β-strand	132	1	30
β-strand	135	1	30
β-strand	140-144	5	30
α-helix	150-160	11
β-strand	161-165	5	30
β-strand	170-175	6	30
α-helix	177-186	10
α-helix	190-200	11
β-strand	201	1	30
α-helix	204-206	3
α-helix	207-215	9
β-strand	224	1	31
β-strand	226-227	2	32
β-strand	232-236	5	32
α-helix	239-247	9
β-strand	314-317	4	32
α-helix	320-332	13
α-helix	336-337	2
β-strand	338	1	31
β-strand	340-341	2	33
α-helix	350	1
β-strand	351	1	34
α-helix	364-373	10
β-strand	379-380	2	33
β-strand	382-385	4	35
α-helix	392-403	12
β-strand	405	1	34
β-strand	407-410	4	35
α-helix	414-427	14
β-strand	435-437	3	36
β-strand	438	1	37
β-strand	443	1	37
β-strand	452-454	3	36
α-helix	458-461	4
α-helix	468-479	12
β-strand	481-487	7	35
α-helix	501-504	4
β-strand	506-514	9	35
α-helix	522-528	7
β-strand	534-537	4	35
α-helix	540-546	7
β-strand	552-559	8	38
α-helix	560-562	3
α-helix	563-571	9
α-helix	574-582	9
α-helix	585-601	17
β-strand	605-608	4	38
α-helix	612-622	11
α-helix	633-644	12
β-strand	651-654	4	38
β-strand	669-672	4	38
α-helix	680-691	12
β-strand	703-710	8	38
α-helix	715-729	15
β-strand	734-736	3	38
α-helix	753-764	12

Chain A: 65 helices, 77 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	43
β-strand	16-18	3	44
α-helix	24-30	7
β-strand	34	1	45
β-strand	64	1	39
β-strand	82-90	9	45
α-helix	96-105	10
β-strand	106-107	2	46
β-strand	112-113	2	46
α-helix	120-127	8
α-helix	133-141	9
β-strand	147	1	47
β-strand	170	1	47
β-strand	175-177	3	48
β-strand	180-182	3	48
β-strand	187	1	49
β-strand	195	1	49
β-strand	201	1	48
α-helix	202-203	2
α-helix	204-212	9
α-helix	216-222	7
β-strand	236-241	6	45
α-helix	261-281	21
α-helix	289-304	16
β-strand	315	1	50
β-strand	321	1	50
α-helix	322-323	2
α-helix	325-329	5
β-strand	343-344	2	51
β-strand	348-350	3	52
β-strand	352	1	53
β-strand	355	1	54
β-strand	363-367	5	52
α-helix	368-373	6
β-strand	376-379	4	41
α-helix	385-394	10
β-strand	402-406	5	41
β-strand	412-414	3	41
α-helix	421-423	3
β-strand	431-434	4	41
β-strand	441-445	5	52
α-helix	449	1
β-strand	455-463	9	52
β-strand	469	1	52
β-strand	470	1	54
α-helix	472-474	3
α-helix	475-478	4
β-strand	486	1	53
β-strand	488-490	3	52
α-helix	495-504	10
β-strand	506	1	52
α-helix	508-510	3
β-strand	512	1	55
β-strand	519	1	55
α-helix	525-534	10
β-strand	541	1	56
α-helix	543-552	10
α-helix	560-563	4
β-strand	565-566	2	57
β-strand	570-571	2	57
β-strand	572	1	56
α-helix	574-581	8
α-helix	583	1
β-strand	587-589	3	58
β-strand	606-608	3	58
β-strand	611-614	4	58
α-helix	619-622	4
α-helix	629-636	8
α-helix	641-658	18
β-strand	663	1	59
α-helix	666-669	4
α-helix	673-698	26
α-helix	710-736	27
α-helix	742-748	7
α-helix	755-762	8
β-strand	766-767	2	60
β-strand	779	1	61
β-strand	782	1	61
α-helix	794-797	4
β-strand	799-800	2	60
α-helix	810-844	35
β-strand	849-850	2	62
β-strand	856-857	2	62
β-strand	863-865	3	62
α-helix	868-870	3
β-strand	873	1	63
β-strand	879	1	64
β-strand	882	1	65
α-helix	890-897	8
β-strand	900	1	66
β-strand	907	1	66
α-helix	908-909	2
β-strand	913	1	67
α-helix	923-946	24
β-strand	953	1	65
β-strand	956	1	64
α-helix	961-971	11
α-helix	978	1
β-strand	979	1	67
α-helix	983-996	14
α-helix	1005-1013	9
α-helix	1016-1025	10
α-helix	1028-1030	3
α-helix	1031-1035	5
α-helix	1039-1055	17
β-strand	1057	1	63
α-helix	1058-1059	2
α-helix	1064-1077	14
α-helix	1097-1105	9
β-strand	1116-1119	4	68
β-strand	1120	1	69
α-helix	1121	1
α-helix	1128-1138	11
β-strand	1141	1	70
α-helix	1143-1146	4
β-strand	1147-1154	8	71
α-helix	1168-1172	5
β-strand	1188	1	72
β-strand	1191-1197	7	71
α-helix	1199-1203	5
α-helix	1209-1220	12
β-strand	1224-1228	5	71
β-strand	1237-1242	6	71
β-strand	1243	1	72
α-helix	1256-1270	15
β-strand	1274	1	70
β-strand	1283-1292	10	68
α-helix	1293	1
β-strand	1298-1307	10	68
α-helix	1316-1318	3
β-strand	1322	1	69
β-strand	1328-1329	2	68
α-helix	1332-1357	26
α-helix	1365-1376	12
α-helix	1396-1399	4
α-helix	1405-1415	11
β-strand	1418-1419	2	44
α-helix	1424-1429	6
α-helix	1432-1434	3
β-strand	1437	1	73
β-strand	1441-1445	5	74
α-helix	1447-1452	6

20 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 XPD/RAD3	0	protein	778	Saccharomyces cerevisiae	P06839 (AlphaFold model)
General transcription and DNA repair factor IIH subunit TFB1	1	protein	642	Saccharomyces cerevisiae	P32776 (AlphaFold model)
General transcription and DNA repair factor IIH subunit TFB2	2	protein	513	Saccharomyces cerevisiae	Q02939 (AlphaFold model)
General transcription and DNA repair factor IIH subunit TFB4	4	protein	338	Saccharomyces cerevisiae	Q12004 (AlphaFold model)
General transcription and DNA repair factor IIH subunit SSL1	6	protein	461	Saccharomyces cerevisiae	Q04673
General transcription and DNA repair factor IIH helicase subunit XPB	7	protein	843	Saccharomyces cerevisiae	Q00578
Transcription initiation factor IIB	M	protein	345	Saccharomyces cerevisiae	P29055
DNA-directed RNA polymerase II subunit RPB1	A	protein	1733	Saccharomyces cerevisiae	P04050
DNA-directed RNA polymerase II subunit RPB2	B	protein	1224	Saccharomyces cerevisiae	P08518
DNA-directed RNA polymerase II subunit RPB3	C	protein	318	Saccharomyces cerevisiae	P16370
DNA-directed RNA polymerase II subunit RPB4	D	protein	221	Saccharomyces cerevisiae	P20433
DNA-directed RNA polymerases I, II, and III subunit RPABC1	E	protein	215	Saccharomyces cerevisiae	P20434

18 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>8UOT_1 General transcription and DNA repair factor IIH helicase subunit XPD/RAD3 (chains 0)
MKFYIDDLPVLFPYPKIYPEQYNYMCDIKKTLDVGGNSILEMPSGTGKTVSLLSLTIAYQ
MHYPEHRKIIYCSRTMSEIEKALVELENLMDYRTKELGYQEDFRGLGLTSRKNLCLHPEV
SKERKGTVVDEKCRRMTNGQAKRKLEEDPEANVELCEYHENLYNIEVEDYLPKGVFSFEK
LLKYCEEKTLCPYFIVRRMISLCNIIIYSYHYLLDPKIAERVSNEVSKDSIVIFDEAHNI
DNVCIESLSLDLTTDALRRATRGANALDERISEVRKVDSQKLQDEYEKLVQGLHSADILT
DQEEPFVETPVLPQDLLTEAIPGNIRRAEHFVSFLKRLIEYLKTRMKVLHVISETPKSFL
QHLKQLTFIERKPLRFCSERLSLLVRTLEVTEVEDFTALKDIATFATLISTYEEGFLLII
EPYEIENAAVPNPIMRFTCLDASIAIKPVFERFSSVIITSGTISPLDMYPRMLNFKTVLQ
KSYAMTLAKKSFLPMIITKGSDQVAISSRFEIRNDPSIVRNYGSMLVEFAKITPDGMVVF
FPSYLYMESIVSMWQTMGILDEVWKHKLILVETPDAQETSLALETYRKACSNGRGAILLS
VARGKVSEGIDFDHQYGRTVLMIGIPFQYTESRILKARLEFMRENYRIRENDFLSFDAMR
HAAQCLGRVLRGKDDYGVMVLADRRFSRKRSQLPKWIAQGLSDADLNLSTDMAISNTKQF
LRTMAQPTDPKDQEGVSVWSYEDLIKHQNSRKDQGGFIENENKEGEQDEDEDEDIEMQ

Sequence of entity 2 (1), FASTA

>8UOT_2 General transcription and DNA repair factor IIH subunit TFB1 (chains 1)
MSHSGAAIFEKVSGIIAINEDVSPAELTWRSTDGDKVHTVVLSTIDKLQATPASSEKMML
RLIGKVDESKKRKDNEGNEVVPKPQRHMFSFNNRTVMDNIKMTLQQIISRYKDADIYEEK
RRREESAQHTETPMSSSSVTAGTPTPHLDTPQLNNGAPLINTAKLDDSLSKEKLLTNLKL
QQSLLKGNKVLMKVFQETVINAGLPPSEFWSTRIPLLRAFALSTSQKVGPYNVLSTIKPV
ASSENKVNVNLSREKILNIFENYPIVKKAYTDNVPKNFKEPEFWARFFSSKLFRKLRGEK
IMQNDRGDVIIDRYLTLDQEFDRKDDDMLLHPVKKIIDLDGNIQDDPVVRGNRPDFTMQP
GVDINGNSDGTVDILKGMNRLSEKMIMALKNEYSRTNLQNKSNITNDEEDEDNDERNELK
IDDLNESYKTNYAIIHLKRNAHEKTTDNDAKSSADSIKNADLKVSNQQMLQQLSLVMDNL
INKLDLNQVVPNNEVSNKINKRVITAIKINAKQAKHNNVNSALGSFVDNTSQANELEVKS
TLPIDLLESCRMLHTTCCEFLKHFYIHFQSGEQKQASTVKKLYNHLKDCIEKLNELFQDV
LNGDGESMSNTCTAYLKPVLNSITLATHKYDEYFNEYNNNSN

Sequence of entity 3 (2), FASTA

>8UOT_3 General transcription and DNA repair factor IIH subunit TFB2 (chains 2)
MSDYSLKHSVTQYLEEIPQQVQNRLYTSPATCLAIYRILPPLAKFFIMAMVFNENEVPLL
DLDKWVNSNGKLQFQNAIKSMKSLHLLIPNKSSGTLMINLNPTFKISLRNALTGGEVQNS
FGVVVEENVVSLDLLDEYSANKWETILHFMVGTPLAKIPSEKVLNLLKHSKLMEEVNSTG
EFKITNEGFQFLLQEINSQLWTLLLQYLKMIETSKMDLVDVLHFIFMLGALEVGKAYKID
ALSETQRIMLQDMRDYGLVFQKHSNDSIFYPTKLALMLTSDTKTIRSASNAMDSVLRQNR
EEPSVNEDGANGKSTTDITTSDDLNKAGLKNQDIPDGSLIVETNFKIYSYSNSPLQIAVL
SLFVHLKARFVNMVLGQITRESIRRALTNGITADQIIAYLETHAHPQMRRLAEEKLEKKL
ELDPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGV
LLWKDDKKKKFFISKEGNSQVLDFAKRKLKKKQ

Sequence of entity 4 (4), FASTA

>8UOT_4 General transcription and DNA repair factor IIH subunit TFB4 (chains 4)
MDAISDPTFKHARSRKQVTEESPSLLTVIIEIAPKLWTTFDEEGNEKGSIIKVLEALIVF
LNAHLAFNSANKVAVIAAYSQGIKYLYPESTSALKASESENKTRSDLKIINSDMYRRFRN
VDETLVEEIYKLFELEKKQIEQNSQRSTLAGAMSAGLTYVNRISKESVTTSLKSRLLVLT
CGSGSSKDEIFQYIPIMNCIFSATKMKCPIDVVKIGGSKESTFLQQTTDATNGVYLHVES
TEGLIQYLATAMFIDPSLRPIIVKPNHGSVDFRTSCYLTGRVVAVGFICSVCLCVLSIIP
PGNKCPACDSQFDEHVIAKLKRKPVVPRLKAKKKVTKP

Sequence of entity 5 (6), FASTA

>8UOT_5 General transcription and DNA repair factor IIH subunit SSL1 (chains 6)
MAPVVISESEEDEDRVAITRRTKRQVHFDGEGDDRVDQQQQQHSSSHRDRDKHVQRKKKK
RLSNRNLQGSNGGYAWEDEIKRSWDLVKVDDEGDMASLVASIVEARKKRTAKKNITPYQR
GIIRSLILTLDCSEAMLEKDLRPNRHAMIIQYAIDFVHEFFDQNPISQMGIIIMRNGLAQ
LVSQVSGNPQDHIDALKSIRKQEPKGNPSLQNALEMARGLLLPVPAHCTREVLIVFGSLS
TTDPGDIHQTIDSLVSEKIRVKVLGLSAQVAICKELCKATNYGDESFYKILLDETHLKEL
FNEAVTPLPVNKINKGFTLVKMGFPTRIFEDTPTFCSCHSKLVYGGYFCPNCHSKVCSLP
TVCPCCDLMLILSTHLARSYHHLMPLKTFAEVPTTEKFRSEDCFSCQSRFPILKNHKNGK
LLTSSRYRCEDCKQEFCVDCDVFIHEILHNCPGCESKPVIT

Sequence of entity 6 (7), FASTA

>8UOT_6 General transcription and DNA repair factor IIH helicase subunit XPB (chains 7)
MTDVEGYQPKSKGKIFPDMGESFFSSDEDSPATDAEIDENYDDNRETSEGRGERDTGAMV
TGLKKPRKKTKSSRHTAADSSMNQMDAKDKALLQDTNSDIPADFVPDSVSGMFRSHDFSY
LRLRPDHASRPLWISPSDGRIILESFSPLAEQAQDFLVTIAEPISRPSHIHEYKITAYSL
YAAVSVGLETDDIISVLDRLSKVPVAESIINFIKGATISYGKVKLVIKHNRYFVETTQAD
ILQMLLNDSVIGPLRIDSDHQVQPPEDVLQQQLQQTAGKPATNVNPNDVEAVFSAVIGGD
NEREEEDDDIDAVHSFEIANESVEVVKKRCQEIDYPVLEEYDFRNDHRNPDLDIDLKPST
QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGITAACTIKKSVIVLCTSSVSVMQW
RQQFLQWCTLQPENCAVFTSDNKEMFQTESGLVVSTYSMVANTRNRSHDSQKVMDFLTGR
EWGFIILDEVHVVPAAMFRRVVSTIAAHAKLGLTATLVREDDKIGDLNFLIGPKLYEANW
MELSQKGHIANVQCAEVWCPMTAEFYQEYLRETARKRMLLYIMNPTKFQACQFLIQYHER
RGDKIIVFSDNVYALQEYALKMGKPFIYGSTPQQERMNILQNFQYNDQINTIFLSKVGDT
SIDLPEATCLIQISSHYGSRRQEAQRLGRILRAKRRNDEGFNAFFYSLVSKDTQEMYYST
KRQAFLVDQGYAFKVITHLHGMENIPNLAYASPRERRELLQEVLLKNEEAAGIEVGDDAD
NSVGRGSNGHKRFKSKAVRGEGSLSGLAGGEDMAYMEYSTNKNKELKEHHPLIRKMYYKN
LKK

Sequence of entity 7 (M), FASTA

>8UOT_7 Transcription initiation factor IIB (chains M)
MMTRESIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTR
SEWRTFSNDDHNGDDPSRVGEASNPLLDGNNLSTRIGKGETTDMRFTKELNKAQGKNVMD
KKDNEVQAAFAKITMLCDAAELPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGC
RRAEVARTFKEIQSLIHVKTKEFGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIP
RFCSHLGLPMQVTTSAEYTAKKCKEIKEIAGKSPITIAVVSIYLNILLFQIPITAAKVGQ
TLQVTEGTIKSGYKILYEHRDKLVDPQLIANGVVSLDNLPGVEKK

Sequence of entity 8 (A), FASTA

>8UOT_8 DNA-directed RNA polymerase II subunit RPB1 (chains A)
MVGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGS
IDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNE
LMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLK
LVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLP
VPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHV
ATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLE
LDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKR
AGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNA
DFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTF
IELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSP
KDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHN
GFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVR
FLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFV
DRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRR
LVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVD
LLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNI
RRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCC
LLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMT
LNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEH
TTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRA
AMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHML
KKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVP
GIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGG
LTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGA
FDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGS
NDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTS
PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS
PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSP
SYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR

Sequence of entity 9 (B), FASTA

>8UOT_9 DNA-directed RNA polymerase II subunit RPB2 (chains B)
MSDLANSEKYYDEDPYGFEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQ
DIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLR
NLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCY
LSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEI
RSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEH
ICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEF
LPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTL
FKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVS
QVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLS
LMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETL
RTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAK
LMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEEND
LDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGV
FLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMI
MNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIA
PGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDG
LKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSR
MTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKK
LMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIA
HGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAA
KLLFQELMAMNITPRLYTDRSRDF

Sequence of entity 10 (C), FASTA

>8UOT_10 DNA-directed RNA polymerase II subunit RPB3 (chains C)
MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLAD
EFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVI
VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEY
DPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPV
DQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPY
SNASQMGNTGSGGYDNAW

Sequence of entity 11 (D), FASTA

>8UOT_11 DNA-directed RNA polymerase II subunit RPB4 (chains D)
MNVSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIK
EALVERRRAFKRSQKKHKKKHLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETRE
KELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQL
GSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY

Sequence of entity 12 (E), FASTA

>8UOT_12 DNA-directed RNA polymerases I, II, and III subunit RPABC1 (chains E)
MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSF
QANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSA
MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQR
ADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	1
ZN	Zinc ion	Zn	15
MG	Magnesium ion	Mg	2

Primary citation

Transcription start site scanning requires the fungi-specific hydrophobic loop of Tfb3. Yang, C., Basnet, P., Sharmin, S. et al. Nucleic Acids Res (2024) 52:11602-11611. DOI 10.1093/nar/gkae805 · PubMed

Other PDB entries of the same protein (UniProt P06839 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7O4J 2.9 Å, Yeast RNA polymerase II transcription pre-initiation complex (consensus)
7ML0 3.0 Å, RNA polymerase II pre-initiation complex (PIC1)
8CEN 3.0 Å, Yeast RNA polymerase II transcription pre-initiation complex with core Mediator
7ML4 3.1 Å, RNA polymerase II initially transcribing complex (ITC)
7ZS9 3.1 Å, Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome…
7O4I 3.2 Å, Yeast RNA polymerase II transcription pre-initiation complex with initial transcription…
7O75 3.2 Å, Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA
7ML2 3.4 Å, RNA polymerase II pre-initiation complex (PIC3)
7O4L 3.4 Å, Yeast TFIIH in the expanded state within the pre-initiation complex
7O72 3.4 Å, Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA
7O73 3.4 Å, Yeast RNA polymerase II transcription pre-initiation complex with closed distorted…
7O4K 3.6 Å, Yeast TFIIH in the contracted state within the pre-initiation complex

Browse structure collections

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