9KD9: DNA-directed RNA polymerase II subunit RPB1

Name: PDB 9KD9: The structure of RNA polymerase II elongation complex paused at N-5 state by actinomycin D.
Published: 2025-11-05
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

The structure of RNA polymerase II elongation complex paused at N-5 state by actinomycin D. Determined by electron microscopy at 2.88 Å resolution. Released 5 Nov 2025.

Method: Electron microscopy
Resolution: 2.88 Å
Organisms: Saccharomyces cerevisiae S288C, Streptomyces sp., synthetic construct
Chains: 16
Atoms: 32,956
Mol. weight: 549.89 kDa
Ligands: MG, ZN
Released: 5 Nov 2025

Explore 9KD9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KD9 contains 190 α-helices and 233 β-strands across 13 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: 79 helices, 65 β-strands

Element	Residues	Length	Sheet
α-helix	10	1
β-strand	11	1	1
β-strand	16-18	3	2
α-helix	24-30	7
β-strand	34	1	3
β-strand	37	1	4
β-strand	41	1	5
β-strand	48	1	5
α-helix	49	1
β-strand	52	1	4
α-helix	56-58	3
β-strand	82-91	10	3
α-helix	96-103	8
β-strand	106	1	6
β-strand	113	1	6
α-helix	122-127	6
α-helix	131-142	12
β-strand	151-153	3	7
β-strand	161-163	3	7
α-helix	171-172	2
β-strand	173-177	5	8
β-strand	180-185	6	8
α-helix	186-187	2
β-strand	198-201	4	8
α-helix	204-212	9
α-helix	216-221	6
α-helix	231-234	4
β-strand	235-241	7	3
α-helix	261-282	22
α-helix	286-304	19
α-helix	312-313	2
β-strand	315	1	9
β-strand	321	1	9
α-helix	325-329	5
α-helix	335	1
α-helix	336-340	5
β-strand	343-345	3	10
β-strand	348-355	8	11
β-strand	363-367	5	11
α-helix	368-373	6
β-strand	375-379	5	12
α-helix	385-394	10
β-strand	402-406	5	12
β-strand	412-414	3	12
α-helix	419-421	3
β-strand	431-435	5	12
β-strand	441-445	5	11
α-helix	452-454	3
β-strand	455-463	9	11
β-strand	468-470	3	11
α-helix	475-478	4
β-strand	486-490	5	11
α-helix	495-504	10
β-strand	506	1	11
α-helix	508-510	3
β-strand	512-513	2	13
β-strand	518-519	2	13
α-helix	526-534	9
β-strand	540-541	2	14
α-helix	543-551	9
α-helix	560-563	4
β-strand	565-567	3	15
β-strand	571	1	15
β-strand	572-573	2	14
α-helix	574-581	8
α-helix	583	1
β-strand	588-590	3	16
β-strand	605-608	4	16
β-strand	611-614	4	16
α-helix	619-622	4
α-helix	629-636	8
α-helix	639-658	20
β-strand	663	1	17
α-helix	667-669	3
α-helix	673-698	26
α-helix	702-705	4
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
α-helix	775-776	2
α-helix	794-797	4
β-strand	799-800	2	18
α-helix	810-845	36
β-strand	849-850	2	20
β-strand	856-857	2	20
β-strand	863-865	3	20
α-helix	868-870	3
β-strand	873	1	21
α-helix	875-877	3
β-strand	879-882	4	22
α-helix	890-897	8
α-helix	910-912	3
β-strand	913	1	23
α-helix	924-946	23
β-strand	953-956	4	22
α-helix	960-971	12
α-helix	978	1
β-strand	979	1	23
α-helix	983-996	14
α-helix	1005-1025	21
α-helix	1028-1029	2
α-helix	1030-1035	6
α-helix	1039-1055	17
β-strand	1057	1	21
α-helix	1058-1059	2
α-helix	1064-1077	14
α-helix	1097-1105	9
β-strand	1115-1119	5	24
β-strand	1120	1	25
α-helix	1121	1
α-helix	1122-1124	3
α-helix	1128-1138	11
α-helix	1143-1145	3
β-strand	1147-1154	8	26
α-helix	1167-1176	10
α-helix	1185-1187	3
β-strand	1188-1197	10	26
α-helix	1199-1204	6
α-helix	1209-1220	12
α-helix	1221-1223	3
β-strand	1224-1228	5	26
β-strand	1237-1243	7	26
α-helix	1244-1245	2
α-helix	1252-1269	18
β-strand	1281-1292	12	24
β-strand	1298-1309	12	24
α-helix	1313-1317	5
β-strand	1322	1	25
β-strand	1328-1329	2	24
α-helix	1332-1338	7
α-helix	1341-1358	18
α-helix	1365-1375	11
α-helix	1389-1391	3
α-helix	1396-1399	4
α-helix	1405-1415	11
β-strand	1418-1419	2	2
α-helix	1424-1429	6
α-helix	1437-1439	3
β-strand	1441-1445	5	27
α-helix	1447-1453	7

Chain B: 53 helices, 84 β-strands

Element	Residues	Length	Sheet
α-helix	23	1
β-strand	24	1	28
α-helix	25	1
α-helix	29-40	12
α-helix	45-53	9
α-helix	54-58	5
α-helix	59-64	6
β-strand	68-73	6	29
α-helix	80-82	3
β-strand	84-97	14	29
β-strand	101-102	2	30
β-strand	110-111	2	30
α-helix	114-120	7
β-strand	125-140	16	29
α-helix	146-147	2
β-strand	150-151	2	29
β-strand	156	1	29
β-strand	164-171	8	29
α-helix	186-191	6
β-strand	203-205	3	31
β-strand	208-212	5	31
β-strand	214-218	5	32
α-helix	219	1
β-strand	223-227	5	33
β-strand	234-242	9	33
β-strand	252-259	8	33
β-strand	269-272	4	33
β-strand	276	1	34
β-strand	280-281	2	33
α-helix	282-289	8
α-helix	294-301	8
α-helix	308-321	14
α-helix	327-337	11
β-strand	338	1	34
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	32
α-helix	409-437	29
α-helix	450-462	13
β-strand	480-482	3	31
α-helix	483-484	2
α-helix	488-495	8
β-strand	497-499	3	32
α-helix	516-518	3
β-strand	522	1	35
β-strand	533	1	32
β-strand	536-538	3	32
β-strand	539	1	35
β-strand	540	1	36
β-strand	544-545	2	37
α-helix	552-560	9
α-helix	563	1
β-strand	564-565	2	38
β-strand	578-582	5	38
β-strand	585-590	6	38
α-helix	593-605	13
β-strand	614-618	5	38
β-strand	623-627	5	38
β-strand	633-639	7	37
β-strand	640-641	2	39
β-strand	650-651	2	39
β-strand	654	1	28
α-helix	655-668	14
α-helix	681-686	6
β-strand	690-694	5	37
α-helix	697-700	4
β-strand	703-704	2	37
α-helix	707-710	4
α-helix	728-729	2
β-strand	740-741	2	37
α-helix	745-748	4
β-strand	750	1	36
α-helix	759-761	3
α-helix	764-774	11
β-strand	777	1	40
α-helix	785-787	3
β-strand	792-796	5	41
β-strand	800	1	42
β-strand	804-805	2	43
α-helix	807-809	3
β-strand	821-827	7	44
β-strand	828	1	17
β-strand	839-842	4	44
α-helix	843-847	5
β-strand	853-862	10	41
β-strand	865	1	45
β-strand	871	1	45
β-strand	873-874	2	46
β-strand	883	1	46
β-strand	898	1	47
α-helix	899-900	2
β-strand	904-905	2	41
β-strand	910-912	3	47
β-strand	914-917	4	46
β-strand	924	1	48
β-strand	928	1	48
β-strand	934-936	3	46
β-strand	939-940	2	47
α-helix	941-942	2
β-strand	947-956	10	41
β-strand	962-972	11	41
β-strand	979-982	4	44
β-strand	987-994	8	44
β-strand	1001	1	49
β-strand	1010-1012	3	44
α-helix	1016-1020	5
α-helix	1023-1038	16
β-strand	1042-1043	2	43
α-helix	1052-1061	10
β-strand	1069-1070	2	44
β-strand	1073	1	49
α-helix	1079	1
β-strand	1080	1	49
α-helix	1081	1
α-helix	1084	1
β-strand	1085-1094	10	44
β-strand	1095	1	40
α-helix	1099-1101	3
β-strand	1104-1106	3	11
β-strand	1111	1	50
β-strand	1118	1	50
α-helix	1122-1124	3
β-strand	1128-1130	3	10
α-helix	1132-1140	9
α-helix	1144-1148	5
α-helix	1149-1153	5
β-strand	1158-1163	6	1
β-strand	1172-1174	3	51
β-strand	1179-1181	3	51
β-strand	1182	1	52
β-strand	1187	1	52
β-strand	1191-1196	6	1
α-helix	1198-1208	11
β-strand	1215-1217	3	2

Chain C: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	53
β-strand	17-23	7	53
α-helix	27-39	13
β-strand	43-54	12	54
α-helix	60-68	9
β-strand	72-74	3	55
α-helix	77-79	3
β-strand	97-104	8	54
β-strand	111-114	4	56
β-strand	119-120	2	54
β-strand	129-132	4	55
α-helix	133	1
β-strand	143-147	5	56
β-strand	152-162	11	54
α-helix	168-170	3
β-strand	176-180	5	53
α-helix	197-200	4
α-helix	202-204	3
α-helix	205-209	5
α-helix	211-213	3
α-helix	218-219	2
β-strand	228-233	6	53
α-helix	240-266	27

Chain D: 9 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
β-strand	23	1	57
β-strand	28	1	57
β-strand	36-38	3	58
β-strand	44-46	3	58
β-strand	49	1	59
α-helix	52-72	21
α-helix	119-133	15
α-helix	139-150	12
α-helix	157-169	13
α-helix	174-182	9
α-helix	188-194	7
α-helix	196-198	3
α-helix	204-216	13

Chain E: 12 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	3-26	24
β-strand	28	1	60
α-helix	32-35	4
α-helix	39-46	8
β-strand	47	1	61
β-strand	53	1	61
β-strand	60-62	3	62
β-strand	64	1	60
α-helix	66-71	6
β-strand	78-82	5	62
β-strand	87-88	2	63
α-helix	90-102	13
β-strand	107-112	6	62
β-strand	115-116	2	63
α-helix	118-121	4
β-strand	131-136	6	62
α-helix	144-146	3
β-strand	152-155	4	64
α-helix	156-157	2
α-helix	158-167	10
α-helix	176	1
β-strand	177-178	2	64
α-helix	183-188	6
α-helix	194	1
β-strand	195-200	6	64
β-strand	208-214	7	64

Chain F: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	73	1	27
α-helix	76-78	3
β-strand	84	1	65
α-helix	85-86	2
α-helix	87-102	16
α-helix	117-126	10
β-strand	132-137	6	27
α-helix	138	1
β-strand	143-147	5	27
β-strand	152	1	65

Chain G: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-13	12	59
α-helix	15-17	3
α-helix	22-30	9
β-strand	37-39	3	59
β-strand	43-49	7	59
β-strand	55	1	59
β-strand	61	1	59
α-helix	62	1
β-strand	68-79	12	59
β-strand	85-94	10	66
β-strand	98-103	6	66
β-strand	106-111	6	66
α-helix	112-114	3
β-strand	120-122	3	67
β-strand	129-131	3	67
β-strand	136-137	2	67
β-strand	142-151	10	66
β-strand	158-162	5	66
β-strand	170	1	66

Chain H: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	15
β-strand	23-30	8	15
β-strand	37-43	7	15
β-strand	54-60	7	15
β-strand	64	1	68
α-helix	67-68	2
α-helix	78-79	2
α-helix	81-83	3
β-strand	88	1	68
α-helix	89-92	4
β-strand	95-105	11	15
β-strand	111-118	8	15
β-strand	121-128	8	15
α-helix	129-132	4
β-strand	139-145	7	15

5 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 S288C	P04050 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB2	B	protein	1224	Saccharomyces cerevisiae S288C	P08518 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB3	C	protein	318	Saccharomyces cerevisiae S288C	P16370 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB4	D	protein	221	Saccharomyces cerevisiae S288C	P20433 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC1	E	protein	215	Saccharomyces cerevisiae S288C	P20434
DNA-directed RNA polymerases I, II, and III subunit RPABC2	F	protein	155	Saccharomyces cerevisiae S288C	P20435
DNA-directed RNA polymerase II subunit RPB7	G	protein	171	Saccharomyces cerevisiae S288C	P34087
DNA-directed RNA polymerases I, II, and III subunit RPABC3	H	protein	146	Saccharomyces cerevisiae S288C	P20436
DNA-directed RNA polymerase II subunit RPB9	I	protein	122	Saccharomyces cerevisiae S288C	P27999
DNA-directed RNA polymerases I, II, and III subunit RPABC5	J	protein	70	Saccharomyces cerevisiae S288C	P22139
DNA-directed RNA polymerase II subunit RPB11	K	protein	120	Saccharomyces cerevisiae S288C	P38902
DNA-directed RNA polymerases I, II, and III subunit RPABC4	L	protein	70	Saccharomyces cerevisiae S288C	P40422

4 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>9KD9_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

>9KD9_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

>9KD9_3 DNA-directed RNA polymerase II subunit RPB3 (chains C)
MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLAD
EFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVI
VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEY
DPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPV
DQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPY
SNASQMGNTGSGGYDNAW

Sequence of entity 4 (D), FASTA

>9KD9_4 DNA-directed RNA polymerase II subunit RPB4 (chains D)
MNVSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIK
EALVERRRAFKRSQKKHKKKHLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETRE
KELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQL
GSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY

Sequence of entity 5 (E), FASTA

>9KD9_5 DNA-directed RNA polymerases I, II, and III subunit RPABC1 (chains E)
MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSF
QANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSA
MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQR
ADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM

Sequence of entity 6 (F), FASTA

>9KD9_6 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQ
HEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRI
AMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL

Sequence of entity 7 (G), FASTA

>9KD9_7 DNA-directed RNA polymerase II subunit RPB7 (chains G)
MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGR
ILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLT
FNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAIGSIKEDYLGAI

Sequence of entity 8 (H), FASTA

>9KD9_8 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIA
SSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGG
LLMRLEGNYRNLNNLKQENAYLLIRR

Sequence of entity 9 (I), FASTA

>9KD9_9 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQ
DIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQ
FS

Sequence of entity 10 (J), FASTA

>9KD9_10 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKF
LRYNPLEKRD

Sequence of entity 11 (K), FASTA

>9KD9_11 DNA-directed RNA polymerase II subunit RPB11 (chains K)
MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAA
YKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETEWNLQTLAADDAF

Sequence of entity 12 (L), FASTA

>9KD9_12 DNA-directed RNA polymerases I, II, and III subunit RPABC4 (chains L)
MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKAR
TKRLVQFEAR

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
ZN	Zinc ion	Zn	8

Primary citation

Stepwise transcription stalling by the anti-cancer drug Actinomycin D and insights into short tandem repeat transcription inhibition. Zhao, W., Zhu, L., Liu, Y. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-70612-y · 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…
9QEB 2.26 Å, CryoEM structure of transcribing RNA polymerase II elongation complex
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…

Browse structure collections

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