9QEB: DNA-directed RNA polymerase II subunit RPB1

CryoEM structure of transcribing RNA polymerase II elongation complex. Determined by electron microscopy at 2.26 Å resolution. Released 27 May 2026.

Method: Electron microscopy
Resolution: 2.26 Å
Organism: Saccharomyces cerevisiae
Chains: 15
Atoms: 33,807
Mol. weight: 545.17 kDa
Ligands: ATP, ZN, MG
Released: 27 May 2026

Explore 9QEB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9QEB contains 194 α-helices and 226 β-strands across 12 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: 80 helices, 67 β-strands

Element	Residues	Length	Sheet
α-helix	10	1
β-strand	11	1	1
β-strand	16-18	3	2
β-strand	21	1	3
α-helix	24-30	7
β-strand	34	1	4
α-helix	56-58	3
β-strand	82-91	10	4
α-helix	93-95	3
α-helix	96-105	10
β-strand	106	1	5
β-strand	113	1	5
α-helix	120-126	7
α-helix	131-142	12
β-strand	147	1	6
β-strand	170	1	6
α-helix	171-172	2
β-strand	175-177	3	7
β-strand	180-183	4	7
β-strand	200-202	3	7
α-helix	203	1
α-helix	204-212	9
α-helix	216-221	6
β-strand	225	1	8
β-strand	229	1	8
α-helix	231-234	4
β-strand	235-241	7	4
β-strand	252	1	9
β-strand	256	1	9
α-helix	261-282	22
α-helix	289-304	16
α-helix	312-314	3
β-strand	315	1	10
β-strand	321	1	10
α-helix	322	1
α-helix	325-329	5
α-helix	335-339	5
β-strand	343-345	3	11
β-strand	348-355	8	12
β-strand	363-367	5	12
α-helix	368-373	6
β-strand	375-379	5	13
α-helix	385-394	10
β-strand	402-406	5	13
β-strand	412-414	3	13
β-strand	431-435	5	13
α-helix	436	1
β-strand	441-445	5	12
α-helix	452-454	3
β-strand	455-463	9	12
β-strand	468-470	3	12
α-helix	472-474	3
α-helix	475-478	4
β-strand	486-490	5	12
α-helix	495-504	10
β-strand	506	1	12
α-helix	507-510	4
β-strand	512-513	2	14
β-strand	518-519	2	14
α-helix	525-535	11
β-strand	540-541	2	15
α-helix	543-552	10
α-helix	560-563	4
β-strand	565	1	16
β-strand	571	1	16
β-strand	572-573	2	15
α-helix	574-581	8
α-helix	583	1
β-strand	588-590	3	17
β-strand	605-608	4	17
β-strand	611-614	4	17
α-helix	619-622	4
α-helix	629-636	8
α-helix	639-660	22
α-helix	666-669	4
α-helix	673-698	26
α-helix	710-736	27
α-helix	742-749	8
α-helix	755-758	4
α-helix	759-763	5
β-strand	766-767	2	18
β-strand	769-770	2	19
β-strand	773-774	2	19
β-strand	779	1	20
β-strand	782	1	20
β-strand	799-800	2	18
α-helix	810-825	16
α-helix	826-830	5
α-helix	831-845	15
β-strand	849-850	2	21
β-strand	856-857	2	21
β-strand	863-865	3	21
α-helix	868-870	3
β-strand	873	1	22
α-helix	875-877	3
β-strand	878-882	5	23
α-helix	890-897	8
α-helix	907-909	3
α-helix	910-912	3
α-helix	916-919	4
α-helix	924-946	23
β-strand	953-957	5	23
α-helix	960-971	12
α-helix	978-979	2
α-helix	983-994	12
α-helix	1005-1014	10
α-helix	1016-1025	10
α-helix	1028-1029	2
α-helix	1030-1035	6
α-helix	1039-1056	18
β-strand	1057	1	22
α-helix	1058-1059	2
α-helix	1064-1081	18
α-helix	1083-1086	4
α-helix	1092	1
α-helix	1093-1097	5
α-helix	1098-1106	9
β-strand	1116-1119	4	24
β-strand	1120	1	25
α-helix	1131-1138	8
β-strand	1141	1	26
α-helix	1143-1146	4
β-strand	1147-1153	7	27
α-helix	1167-1172	6
β-strand	1192-1197	6	27
α-helix	1199-1205	7
α-helix	1209-1220	12
β-strand	1224-1228	5	27
β-strand	1236-1242	7	27
α-helix	1257-1269	13
β-strand	1274	1	26
β-strand	1282-1292	11	24
β-strand	1298-1308	11	24
α-helix	1313-1316	4
β-strand	1322	1	25
β-strand	1328-1329	2	24
α-helix	1332-1339	8
α-helix	1341-1356	16
α-helix	1365-1374	10
α-helix	1396-1400	5
α-helix	1405-1415	11
α-helix	1417	1
β-strand	1418-1419	2	2
α-helix	1424-1429	6
α-helix	1437-1439	3
β-strand	1441-1445	5	28
α-helix	1447-1451	5

Chain B: 60 helices, 81 β-strands

Element	Residues	Length	Sheet
α-helix	24-26	3
α-helix	27-29	3
α-helix	30-36	7
α-helix	45-53	9
α-helix	54-58	5
α-helix	59-65	7
β-strand	69-73	5	29
α-helix	80-82	3
β-strand	84-97	14	29
β-strand	101-103	3	30
β-strand	109-111	3	30
α-helix	114-120	7
β-strand	125-140	16	29
β-strand	150-155	6	29
α-helix	157-159	3
α-helix	161-163	3
β-strand	165-171	7	29
α-helix	186-191	6
β-strand	203-205	3	31
β-strand	208-210	3	31
β-strand	211-212	2	32
α-helix	213	1
β-strand	214-218	5	33
α-helix	219	1
β-strand	224-227	4	34
β-strand	234-239	6	34
β-strand	242	1	35
β-strand	252	1	35
β-strand	255-260	6	34
β-strand	268-272	5	34
β-strand	276	1	36
β-strand	280-281	2	34
α-helix	282-289	8
α-helix	294-302	9
α-helix	309-320	12
α-helix	327-336	10
β-strand	338	1	36
α-helix	345-354	10
α-helix	355-359	5
α-helix	371-389	19
α-helix	394-397	4
α-helix	401-403	3
β-strand	404-407	4	33
α-helix	409-437	29
α-helix	440-442	3
α-helix	444-447	4
α-helix	450-463	14
β-strand	466	1	37
β-strand	476	1	37
α-helix	477	1
β-strand	480-481	2	32
α-helix	488-494	7
β-strand	497-499	3	33
α-helix	510-512	3
α-helix	514-515	2
α-helix	516-518	3
β-strand	522	1	38
β-strand	536-538	3	33
β-strand	539	1	38
β-strand	544-545	2	39
α-helix	552-560	9
β-strand	564-565	2	40
α-helix	566-568	3
α-helix	577	1
β-strand	578-582	5	40
β-strand	585-590	6	40
α-helix	593-606	14
β-strand	614-618	5	40
β-strand	623-627	5	40
β-strand	633-639	7	39
β-strand	640-641	2	41
β-strand	650-651	2	41
α-helix	655-666	12
α-helix	681-686	6
β-strand	690-694	5	39
α-helix	697-700	4
β-strand	703-704	2	39
α-helix	707-709	3
α-helix	728-729	2
β-strand	740-741	2	39
α-helix	745-748	4
α-helix	753-755	3
α-helix	759-761	3
β-strand	762	1	42
α-helix	764-774	11
β-strand	777	1	43
α-helix	785-787	3
β-strand	792-796	5	44
β-strand	800	1	45
β-strand	804-805	2	46
α-helix	809-812	4
β-strand	821-827	7	47
β-strand	838-842	5	47
α-helix	843-847	5
β-strand	853-861	9	44
β-strand	874	1	48
β-strand	898	1	49
β-strand	904-906	3	44
β-strand	910-912	3	49
β-strand	914	1	48
β-strand	915	1	50
β-strand	936	1	50
β-strand	939-940	2	49
α-helix	941-942	2
β-strand	946-956	11	44
β-strand	962-972	11	44
β-strand	979-981	3	47
β-strand	987-994	8	47
β-strand	1001-1002	2	51
β-strand	1010-1012	3	47
α-helix	1016-1020	5
β-strand	1022	1	42
α-helix	1023-1038	16
α-helix	1040-1041	2
β-strand	1042-1043	2	46
α-helix	1052-1061	10
β-strand	1069-1070	2	47
β-strand	1072-1073	2	51
α-helix	1079	1
β-strand	1080	1	51
α-helix	1081	1
β-strand	1085-1094	10	47
β-strand	1095	1	43
α-helix	1099-1101	3
β-strand	1104-1106	3	12
β-strand	1111	1	52
β-strand	1118	1	52
α-helix	1119	1
α-helix	1127	1
β-strand	1128-1130	3	11
α-helix	1132-1141	10
α-helix	1144-1152	9
β-strand	1158-1163	6	1
β-strand	1172-1174	3	53
β-strand	1179-1181	3	53
β-strand	1182	1	54
β-strand	1187	1	54
β-strand	1191-1196	6	1
α-helix	1198-1209	12
β-strand	1212	1	3
β-strand	1215-1217	3	2

Chain C: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	55
β-strand	17-23	7	55
α-helix	27-39	13
β-strand	43-54	12	56
α-helix	60-68	9
β-strand	72	1	57
α-helix	77-79	3
β-strand	96-104	9	56
α-helix	110	1
β-strand	111-114	4	58
α-helix	115-117	3
β-strand	119-120	2	56
α-helix	131	1
β-strand	132	1	57
α-helix	133	1
β-strand	143-147	5	58
β-strand	152-162	11	56
α-helix	168-170	3
β-strand	176-180	5	55
α-helix	197-200	4
α-helix	202-204	3
α-helix	205-209	5
α-helix	217-219	3
β-strand	228-233	6	55
α-helix	240-265	26

Chain D: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	28
β-strand	23	1	59
β-strand	28	1	59
β-strand	36-38	3	60
β-strand	44-46	3	60
β-strand	48-50	3	28
α-helix	52-72	21
α-helix	119-134	16
α-helix	139-150	12
α-helix	157-168	12
α-helix	174-182	9
α-helix	188-194	7
α-helix	196-198	3
α-helix	204-217	14

Chain E: 12 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	6-25	20
β-strand	28	1	61
α-helix	32-35	4
α-helix	39-43	5
β-strand	47	1	62
β-strand	53	1	62
α-helix	55-58	4
β-strand	60-62	3	63
β-strand	64	1	61
α-helix	66-71	6
β-strand	78-82	5	63
β-strand	88	1	64
α-helix	92-103	12
β-strand	107-112	6	63
β-strand	116	1	64
α-helix	118-123	6
β-strand	131-136	6	63
α-helix	138-140	3
α-helix	144-146	3
β-strand	152-155	4	65
α-helix	158-167	10
α-helix	172-174	3
β-strand	177-178	2	65
α-helix	183-188	6
β-strand	195-201	7	65
β-strand	207-214	8	65

Chain F: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	73	1	28
β-strand	84	1	66
α-helix	85-86	2
α-helix	87-102	16
α-helix	117-126	10
β-strand	132-137	6	28
α-helix	138	1
β-strand	143-147	5	28
β-strand	152	1	66

Chain G: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-13	12	28
α-helix	15-17	3
α-helix	22-34	13
β-strand	38-39	2	28
β-strand	43-49	7	28
β-strand	55	1	28
α-helix	56-58	3
β-strand	60-61	2	28
β-strand	68-79	12	28
β-strand	86-95	10	67
β-strand	98-103	6	67
β-strand	106-111	6	67
α-helix	112-114	3
β-strand	120-122	3	68
β-strand	129-131	3	68
β-strand	136-137	2	68
β-strand	142-152	11	67
β-strand	157-162	6	67
β-strand	169-170	2	67

Chain H: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	16
β-strand	23-30	8	16
β-strand	37-43	7	16
β-strand	54-60	7	16
α-helix	89-92	4
β-strand	95-106	12	16
β-strand	111-118	8	16
β-strand	121-128	8	16
β-strand	139-145	7	16

4 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
DNA-directed RNA polymerase II subunit RPB1	A	protein	1733	Saccharomyces cerevisiae	P04050 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB2	B	protein	1224	Saccharomyces cerevisiae	P08518 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB3	C	protein	318	Saccharomyces cerevisiae	P16370 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB4	D	protein	221	Saccharomyces cerevisiae	P20433 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC1	E	protein	215	Saccharomyces cerevisiae	P20434
DNA-directed RNA polymerases I, II, and III subunit RPABC2	F	protein	155	Saccharomyces cerevisiae	P20435
DNA-directed RNA polymerase II subunit RPB7	G	protein	171	Saccharomyces cerevisiae	P34087
DNA-directed RNA polymerases I, II, and III subunit RPABC3	H	protein	146	Saccharomyces cerevisiae	P20436
DNA-directed RNA polymerase II subunit RPB9	I	protein	122	Saccharomyces cerevisiae	P27999
DNA-directed RNA polymerases I, II, and III subunit RPABC5	J	protein	70	Saccharomyces cerevisiae	P22139
DNA-directed RNA polymerase II subunit RPB11	K	protein	120	Saccharomyces cerevisiae	P38902
DNA-directed RNA polymerases I, II, and III subunit RPABC4	L	protein	70	Saccharomyces cerevisiae	P40422

3 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>9QEB_1 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 2 (B), FASTA

>9QEB_2 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 3 (C), FASTA

>9QEB_3 DNA-directed RNA polymerase II subunit RPB3 (chains C)
MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLAD
EFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVI
VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEY
DPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPV
DQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPY
SNASQMGNTGSGGYDNAW

Sequence of entity 4 (D), FASTA

>9QEB_4 DNA-directed RNA polymerase II subunit RPB4 (chains D)
MNVSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIK
EALVERRRAFKRSQKKHKKKHLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETRE
KELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQL
GSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY

Sequence of entity 5 (E), FASTA

>9QEB_5 DNA-directed RNA polymerases I, II, and III subunit RPABC1 (chains E)
MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSF
QANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSA
MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQR
ADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM

Sequence of entity 6 (F), FASTA

>9QEB_6 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQ
HEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRI
AMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL

Sequence of entity 7 (G), FASTA

>9QEB_7 DNA-directed RNA polymerase II subunit RPB7 (chains G)
MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGR
ILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLT
FNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAIGSIKEDYLGAI

Sequence of entity 8 (H), FASTA

>9QEB_8 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIA
SSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGG
LLMRLEGNYRNLNNLKQENAYLLIRR

Sequence of entity 9 (I), FASTA

>9QEB_9 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQ
DIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQ
FS

Sequence of entity 10 (J), FASTA

>9QEB_10 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKF
LRYNPLEKRD

Sequence of entity 11 (K), FASTA

>9QEB_11 DNA-directed RNA polymerase II subunit RPB11 (chains K)
MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAA
YKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETEWNLQTLAADDAF

Sequence of entity 12 (L), FASTA

>9QEB_12 DNA-directed RNA polymerases I, II, and III subunit RPABC4 (chains L)
MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKAR
TKRLVQFEAR

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
ZN	Zinc ion	Zn	8
MG	Magnesium ion	Mg	2

Water and common crystallization additives (K) are not listed.

Primary citation

Sub-2 angstrom cryo-EM structures of transcribing RNA polymerase II reveal critical roles of water molecules in catalysis. Li, Q., Yi, G., Wu, Y. et al. Mol Cell (2026) 86:1896-1910.e7. DOI 10.1016/j.molcel.2026.04.007 · PubMed

Other PDB entries of the same protein (UniProt P04050 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5VKO 1.8 Å, SPT6 tSH2-RPB1 1468-1500 pT1471, pS1493
9SV6 1.96 Å, CryoEM structure of transcribing RNA polymerase II elongation complex with ATP and Elf1
5VKL 2.2 Å, SPT6 tSH2-RPB1 1476-1500 pS1493
9W8V 2.23 Å, Structure of post-translocation state of yeast Pol II complexed with a cisplatin-induced…
1TWF 2.3 Å, RNA polymerase II complexed with UTP at 2.3 A resolution
9RYB 2.33 Å, CryoEM structure of transcribing RNA polymerase II elongation complex in post-catalysis…
9KD8 2.46 Å, The structure of RNA polymerase II elongation complex paused at N-2 state by actinomycin…
6NPW 2.49 Å, SSu72/Sympk in complex with Ser2/Ser5 phosphorylated peptide
9K7F 2.5 Å, RNA polymerase II elongation complex apo structure.
30ES 2.54 Å, Cryo-EM structure of the yeast RNA polymerase II elongation complex with 19-mer RNA in…
30EP 2.55 Å, Cryo-EM structure of the yeast RNA polymerase II elongation complex with 19-mer RNA in…
9W8T 2.56 Å, Structure of yeast Pol II in complex with a cisplatin-induced inter-strand crosslink…

Browse structure collections

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