8CEO: PDB entry 8CEO

Name: PDB 8CEO: Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome
Published: 2023-03-08
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome. Determined by electron microscopy at 3.6 Å resolution. Released 8 Mar 2023.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Saccharomyces cerevisiae, synthetic construct, Xenopus laevis
Chains: 54
Atoms: 113,584
Mol. weight: 2102.67 kDa
Ligands: SF4, MG, ZN
Released: 8 Mar 2023

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

Secondary structure: helices and β-sheets

8CEO contains 632 α-helices and 568 β-strands across 52 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, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	1
β-strand	8-11	4	1
β-strand	17	1	2
α-helix	19-34	16
β-strand	37-41	5	3
α-helix	42-43	2
β-strand	45	1	4
α-helix	48-62	15
β-strand	69-73	5	3
α-helix	76-97	22
β-strand	104-107	4	3
α-helix	112-114	3
α-helix	126-137	12
α-helix	140-147	8
α-helix	157-160	4
α-helix	161-163	3
β-strand	174-176	3	3
α-helix	178-188	11
α-helix	192-198	7
β-strand	205-209	5	3
α-helix	211-214	4
α-helix	216-225	10
β-strand	231-235	5	3
α-helix	237-239	3
α-helix	240-247	8
β-strand	250-253	4	5
α-helix	254-277	24
α-helix	280-291	12
α-helix	295-298	4
α-helix	313-315	3
α-helix	328-346	19
β-strand	352-354	3	5
α-helix	356-367	12
α-helix	371-375	5
α-helix	377-388	12
α-helix	394-396	3
α-helix	397-411	15
β-strand	416-421	6	5
β-strand	434-439	6	5
α-helix	443-452	10
β-strand	456-459	4	3
α-helix	468-472	5
β-strand	477-482	6	3
β-strand	492-497	6	6
β-strand	499	1	7
β-strand	505	1	7
α-helix	510-512	3
α-helix	516-532	17
β-strand	536-541	6	6
α-helix	544-557	14
α-helix	559-563	5
β-strand	568-571	4	6
α-helix	576-591	16
β-strand	596-601	6	6
α-helix	614-616	3
β-strand	618-623	6	6
α-helix	633-646	14
α-helix	650-666	17
β-strand	671	1	4
β-strand	677-682	6	6
α-helix	684-689	6
α-helix	695-700	6
α-helix	703-705	3
β-strand	708	1	6
α-helix	710-723	14
α-helix	727-729	3
β-strand	739	1	2
α-helix	741-751	11

Chain 1: 33 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	12
β-strand	12-19	8	12
β-strand	26-31	6	12
β-strand	37-38	2	12
β-strand	41	1	12
β-strand	45-50	6	12
β-strand	59-64	6	12
β-strand	86-91	6	12
α-helix	94-120	27
α-helix	171-176	6
α-helix	178-187	10
α-helix	191-195	5
α-helix	196-200	5
α-helix	206-211	6
α-helix	214-225	12
α-helix	228-230	3
α-helix	233-236	4
β-strand	246-251	6	13
α-helix	253-262	10
α-helix	264-271	8
α-helix	280-288	9
α-helix	291-296	6
α-helix	299-301	3
α-helix	311-314	4
α-helix	315-329	15
α-helix	339-343	5
α-helix	352-354	3
α-helix	356-358	3
β-strand	362	1	14
β-strand	368	1	14
α-helix	371-389	19
α-helix	414-419	6
α-helix	426-430	5
β-strand	432	1	15
β-strand	434	1	16
α-helix	441-444	4
α-helix	463-465	3
α-helix	466-482	17
α-helix	486-489	4
α-helix	495-513	19
α-helix	537-539	3
α-helix	544-570	27
α-helix	573-575	3
α-helix	576-604	29
α-helix	609-615	7
α-helix	617-638	22

Chain 2: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	7-16	10
α-helix	19-25	7
α-helix	29-36	8
α-helix	41-51	11
β-strand	57-58	2	17
α-helix	59-65	7
β-strand	66	1	18
α-helix	68-70	3
α-helix	71-83	13
β-strand	87-92	6	17
β-strand	95-100	6	17
α-helix	102-113	12
β-strand	124	1	19
α-helix	131-135	5
α-helix	136-151	16
α-helix	161-168	8
β-strand	175-176	2	20
β-strand	181-182	2	20
α-helix	186-193	8
α-helix	196-210	15
α-helix	218-230	13
β-strand	237-238	2	19
α-helix	239-241	3
α-helix	244-256	13
β-strand	259-260	2	21
β-strand	268-269	2	19
β-strand	270-271	2	21
α-helix	273-276	4
β-strand	338-341	4	22
β-strand	346-350	5	22
α-helix	354-360	7
β-strand	365-369	5	22
β-strand	374-377	4	22
α-helix	380-388	9
α-helix	393-402	10
β-strand	404	1	22
α-helix	406-422	17
α-helix	435-448	14
β-strand	452-459	8	23
β-strand	460	1	24
α-helix	465-477	13
β-strand	481-485	5	23
β-strand	490-494	5	23
α-helix	498-506	9

Chain 3: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	13	1	29
β-strand	18	1	29
β-strand	29-30	2	30
β-strand	38	1	30
α-helix	40-46	7
β-strand	52-53	2	31
β-strand	62-63	2	31
β-strand	69-70	2	30
α-helix	76-89	14
α-helix	103-122	20
α-helix	126-137	12

Chain 4: 16 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	24-30	7	34
α-helix	34-43	10
α-helix	49-67	19
β-strand	72-79	8	34
β-strand	82-87	6	34
α-helix	89-90	2
α-helix	91-96	6
α-helix	116-138	23
α-helix	149-166	18
β-strand	173-180	8	34
α-helix	190-192	3
α-helix	193-205	13
β-strand	210-215	6	34
α-helix	222-230	9
β-strand	235-238	4	34
α-helix	244-250	7
α-helix	256-258	3
β-strand	262	1	18
β-strand	275	1	35
β-strand	282	1	35
α-helix	283	1
β-strand	286-289	4	36
β-strand	295-296	2	36
α-helix	299-300	2
α-helix	301-303	3
β-strand	304	1	37
β-strand	311	1	37
α-helix	314-320	7
α-helix	322-325	4

Chain 5: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	24
β-strand	7-11	5	23
α-helix	14-26	13
β-strand	31-34	4	23
β-strand	39-42	4	23
α-helix	44-46	3
α-helix	47-57	11
α-helix	58-61	4

Chain 6: 21 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	79-80	2
α-helix	97-110	14
β-strand	118	1	16
β-strand	120	1	41
β-strand	124-131	8	42
α-helix	134-137	4
α-helix	145-163	19
β-strand	168-175	8	42
β-strand	178-186	9	42
α-helix	189-201	13
α-helix	203-204	2
α-helix	210-220	11
β-strand	229-236	8	42
α-helix	247-256	10
β-strand	259-265	7	42
α-helix	271-280	10
β-strand	288-290	3	42
α-helix	294-303	10
α-helix	307-308	2
β-strand	309	1	41
α-helix	310	1
β-strand	311	1	15
β-strand	319-323	5	36
β-strand	326-327	2	43
β-strand	334-335	2	44
β-strand	342-343	2	44
β-strand	347-348	2	43
β-strand	355-356	2	43
β-strand	361-362	2	36
β-strand	369-370	2	36
α-helix	373-377	5
α-helix	380-383	4
α-helix	385-389	5
β-strand	390-391	2	45
α-helix	392-393	2
α-helix	397-398	2
β-strand	402	1	46
α-helix	408	1
β-strand	409	1	46
α-helix	410	1
β-strand	427-428	2	45
α-helix	438-444	7
α-helix	452-456	5

Chain 7: 34 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	105-107	3
α-helix	108-110	3
β-strand	117	1	22
α-helix	122-124	3
β-strand	132-134	3	48
β-strand	140-144	5	48
α-helix	151-160	10
β-strand	162-165	4	48
β-strand	170-174	5	48
α-helix	177-185	9
α-helix	190-200	11
β-strand	201	1	48
α-helix	204-206	3
α-helix	207-217	11
β-strand	223-228	6	49
β-strand	231-236	6	49
α-helix	240-244	5
β-strand	251	1	50
β-strand	314-317	4	49
β-strand	318	1	50
α-helix	323-332	10
β-strand	337-338	2	49
β-strand	340-341	2	51
α-helix	350-351	2
β-strand	356	1	52
α-helix	364-373	10
β-strand	379-380	2	51
α-helix	381	1
β-strand	382-385	4	53
α-helix	392-403	12
β-strand	407-411	5	53
α-helix	414-427	14
β-strand	428	1	52
α-helix	432-434	3
β-strand	435-438	4	53
β-strand	452-456	5	53
α-helix	457-460	4
α-helix	468-479	12
β-strand	482	1	54
β-strand	484-488	5	53
α-helix	490-492	3
α-helix	501-504	4
β-strand	507	1	54
β-strand	510-514	5	53
α-helix	522-526	5
α-helix	527-530	4
β-strand	534-537	4	53
α-helix	540-545	6
β-strand	552-557	6	55
β-strand	558-559	2	56
α-helix	560-562	3
α-helix	563-570	8
α-helix	574-582	9
α-helix	585-600	16
β-strand	605-608	4	55
α-helix	612-622	11
β-strand	626-627	2	55
α-helix	633-645	13
β-strand	651-654	4	55
β-strand	669-672	4	55
α-helix	680-687	8
α-helix	694-697	4
β-strand	703-707	5	55
β-strand	709-710	2	56
α-helix	714-729	16
β-strand	734-736	3	55
α-helix	753-766	14
α-helix	832-835	4

44 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	0	protein	778	Saccharomyces cerevisiae	P06839 (AlphaFold model)
TFB1 isoform 1	1	protein	642	Saccharomyces cerevisiae	P32776 (AlphaFold model)
RNA polymerase II transcription factor B subunit 2	2	protein	513	Saccharomyces cerevisiae	Q02939 (AlphaFold model)
RNA polymerase II transcription factor B subunit 3	3	protein	321	Saccharomyces cerevisiae	Q03290 (AlphaFold model)
General transcription and DNA repair factor IIH subunit TFB4	4	protein	338	Saccharomyces cerevisiae	Q12004
General transcription and DNA repair factor IIH subunit TFB5	5	protein	72	Saccharomyces cerevisiae	Q3E7C1
General transcription and DNA repair factor IIH	6	protein	461	Saccharomyces cerevisiae	Q04673
General transcription and DNA repair factor IIH helicase subunit XPB	7	protein	843	Saccharomyces cerevisiae	Q00578
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	347	Saccharomyces cerevisiae	P16370
DNA-directed RNA polymerase II subunit RPB4	D	protein	221	Saccharomyces cerevisiae	P20433

38 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>8CEO_1 General transcription and DNA repair factor IIH helicase subunit XPD (chains 0)
MKFYIDDLPVLFPYPKIYPEQYNYMCDIKKTLDVGGNSILEMPSGTGKTVSLLSLTIAYQ
MHYPEHRKIIYCSRTMSEIEKALVELENLMDYRTKELGYQEDFRGLGLTSRKNLCLHPEV
SKERKGTVVDEKCRRMTNGQAKRKLEEDPEANVELCEYHENLYNIEVEDYLPKGVFSFEK
LLKYCEEKTLCPYFIVRRMISLCNIIIYSYHYLLDPKIAERVSNEVSKDSIVIFDEAHNI
DNVCIESLSLDLTTDALRRATRGANALDERISEVRKVDSQKLQDEYEKLVQGLHSADILT
DQEEPFVETPVLPQDLLTEAIPGNIRRAEHFVSFLKRLIEYLKTRMKVLHVISETPKSFL
QHLKQLTFIERKPLRFCSERLSLLVRTLEVTEVEDFTALKDIATFATLISTYEEGFLLII
EPYEIENAAVPNPIMRFTCLDASIAIKPVFERFSSVIITSGTISPLDMYPRMLNFKTVLQ
KSYAMTLAKKSFLPMIITKGSDQVAISSRFEIRNDPSIVRNYGSMLVEFAKITPDGMVVF
FPSYLYMESIVSMWQTMGILDEVWKHKLILVETPDAQETSLALETYRKACSNGRGAILLS
VARGKVSEGIDFDHQYGRTVLMIGIPFQYTESRILKARLEFMRENYRIRENDFLSFDAMR
HAAQCLGRVLRGKDDYGVMVLADRRFSRKRSQLPKWIAQGLSDADLNLSTDMAISNTKQF
LRTMAQPTDPKDQEGVSVWSYEDLIKHQNSRKDQGGFIENENKEGEQDEDEDEDIEMQ

Sequence of entity 2 (1), FASTA

>8CEO_2 TFB1 isoform 1 (chains 1)
MSHSGAAIFEKVSGIIAINEDVSPAELTWRSTDGDKVHTVVLSTIDKLQATPASSEKMML
RLIGKVDESKKRKDNEGNEVVPKPQRHMFSFNNRTVMDNIKMTLQQIISRYKDADIYEEK
RRREESAQHTETPMSSSSVTAGTPTPHLDTPQLNNGAPLINTAKLDDSLSKEKLLTNLKL
QQSLLKGNKVLMKVFQETVINAGLPPSEFWSTRIPLLRAFALSTSQKVGPYNVLSTIKPV
ASSENKVNVNLSREKILNIFENYPIVKKAYTDNVPKNFKEPEFWARFFSSKLFRKLRGEK
IMQNDRGDVIIDRYLTLDQEFDRKDDDMLLHPVKKIIDLDGNIQDDPVVRGNRPDFTMQP
GVDINGNSDGTVDILKGMNRLSEKMIMALKNEYSRTNLQNKSNITNDEEDEDNDERNELK
IDDLNESYKTNYAIIHLKRNAHEKTTDNDAKSSADSIKNADLKVSNQQMLQQLSLVMDNL
INKLDLNQVVPNNEVSNKINKRVITAIKINAKQAKHNNVNSALGSFVDNTSQANELEVKS
TLPIDLLESCRMLHTTCCEFLKHFYIHFQSGEQKQASTVKKLYNHLKDCIEKLNELFQDV
LNGDGESMSNTCTAYLKPVLNSITLATHKYDEYFNEYNNNSN

Sequence of entity 3 (2), FASTA

>8CEO_3 RNA polymerase II transcription factor B subunit 2 (chains 2)
MSDYSLKHSVTQYLEEIPQQVQNRLYTSPATCLAIYRILPPLAKFFIMAMVFNENEVPLL
DLDKWVNSNGKLQFQNAIKSMKSLHLLIPNKSSGTLMINLNPTFKISLRNALTGGEVQNS
FGVVVEENVVSLDLLDEYSANKWETILHFMVGTPLAKIPSEKVLNLLKHSKLMEEVNSTG
EFKITNEGFQFLLQEINSQLWTLLLQYLKMIETSKMDLVDVLHFIFMLGALEVGKAYKID
ALSETQRIMLQDMRDYGLVFQKHSNDSIFYPTKLALMLTSDTKTIRSASNAMDSVLRQNR
EEPSVNEDGANGKSTTDITTSDDLNKAGLKNQDIPDGSLIVETNFKIYSYSNSPLQIAVL
SLFVHLKARFVNMVLGQITRESIRRALTNGITADQIIAYLETHAHPQMRRLAEEKLEKKL
ELDPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGV
LLWKDDKKKKFFISKEGNSQVLDFAKRKLKKKQ

Sequence of entity 4 (3), FASTA

>8CEO_4 RNA polymerase II transcription factor B subunit 3 (chains 3)
MLMDEYEENKDMCPICKTDRYLSPDVKFLVNPECYHRICESCVDRIFSLGPAQCPYKGCD
KILRKNKFKTQIFDDVEVEKEVDIRKRVFNVFNKTIDDFNGDLVEYNKYLEEVEDIIYKL
DHGIDVAKTEEKLRTYEELNKQLIMNNLERSRTEIESFEQRQKFEKEMKLKKRLLERQIE
EEERMNKEWTKKEIVNRLSTTTQDINETIEGVKNTVKLKKSSARRKLEELNRVLKNNPYF
NSNVNVQNSRLKDAVPFTPFNGDREAHPRFTLKGSVYNDPFIKDLEHRKEFIASGFNTNY
AYERVLTEAFMGLGCVISEEL

Sequence of entity 5 (4), FASTA

>8CEO_5 General transcription and DNA repair factor IIH subunit TFB4 (chains 4)
MDAISDPTFKHARSRKQVTEESPSLLTVIIEIAPKLWTTFDEEGNEKGSIIKVLEALIVF
LNAHLAFNSANKVAVIAAYSQGIKYLYPESTSALKASESENKTRSDLKIINSDMYRRFRN
VDETLVEEIYKLFELEKKQIEQNSQRSTLAGAMSAGLTYVNRISKESVTTSLKSRLLVLT
CGSGSSKDEIFQYIPIMNCIFSATKMKCPIDVVKIGGSKESTFLQQTTDATNGVYLHVES
TEGLIQYLATAMFIDPSLRPIIVKPNHGSVDFRTSCYLTGRVVAVGFICSVCLCVLSIIP
PGNKCPACDSQFDEHVIAKLKRKPVVPRLKAKKKVTKP

Sequence of entity 6 (5), FASTA

>8CEO_6 General transcription and DNA repair factor IIH subunit TFB5 (chains 5)
MARARKGALVQCDPSIKALILQIDAKMSDIVLEELDDTHLLVNPSKVEFVKHELNRLLSK
NIYNPMDEEENQ

Sequence of entity 7 (6), FASTA

>8CEO_7 General transcription and DNA repair factor IIH (chains 6)
MAPVVISESEEDEDRVAITRRTKRQVHFDGEGDDRVDQQQQQHSSSHRDRDKHVQRKKKK
RLSNRNLQGSNGGYAWEDEIKRSWDLVKVDDEGDMASLVASIVEARKKRTAKKNITPYQR
GIIRSLILTLDCSEAMLEKDLRPNRHAMIIQYAIDFVHEFFDQNPISQMGIIIMRNGLAQ
LVSQVSGNPQDHIDALKSIRKQEPKGNPSLQNALEMARGLLLPVPAHCTREVLIVFGSLS
TTDPGDIHQTIDSLVSEKIRVKVLGLSAQVAICKELCKATNYGDESFYKILLDETHLKEL
FNEAVTPLPVNKINKGFTLVKMGFPTRIFEDTPTFCSCHSKLVYGGYFCPNCHSKVCSLP
TVCPCCDLMLILSTHLARSYHHLMPLKTFAEVPTTEKFRSEDCFSCQSRFPILKNHKNGK
LLTSSRYRCEDCKQEFCVDCDVFIHEILHNCPGCESKPVIT

Sequence of entity 8 (7), FASTA

>8CEO_8 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 9 (A), FASTA

>8CEO_9 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 10 (B), FASTA

>8CEO_10 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 11 (C), FASTA

>8CEO_11 DNA-directed RNA polymerase II subunit RPB3 (chains C)
MGSHHHHHHSNSGLNDIFEAQKIEWHEDTGSSEGPQVKIREASKDNVDFILSNVDLAMAN
SLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEYSRDCFCEDH
CDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQ
ELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYED
PPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQDKVN
FASGDNNTASNMLGSNEDVMMTGAEQDPYSNASQMGNTGSGGYDNAW

Sequence of entity 12 (D), FASTA

>8CEO_12 DNA-directed RNA polymerase II subunit RPB4 (chains D)
MNVSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIK
EALVERRRAFKRSQKKHKKKHLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETRE
KELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQL
GSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	1
MG	Magnesium ion	Mg	1
ZN	Zinc ion	Zn	17

Primary citation

Yeast PIC-Mediator structure with RNA polymerase II C-terminal domain. Schilbach, S., Wang, H., Dienemann, C. et al. Proc Natl Acad Sci U S A (2023) 120:e2220542120-e2220542120. DOI 10.1073/pnas.2220542120 · 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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