9S0U: RNA polymerase II subunit D

Name: PDB 9S0U: State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3
Published: 2025-09-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3. Determined by electron microscopy at 6.72 Å resolution. Released 24 Sept 2025.

Method: Electron microscopy
Resolution: 6.72 Å
Organisms: Sus scrofa, synthetic construct, Homo sapiens
Chains: 35
Atoms: 73,121
Mol. weight: 1827.45 kDa
Ligands: ZN, MG
Released: 24 Sept 2025

Explore 9S0U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9S0U contains 380 α-helices and 399 β-strands across 32 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: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	36	1	22
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	72
α-helix	87-113	27
β-strand	118-119	2	73
α-helix	121-131	11

Chain A: 75 helices, 69 β-strands

Element	Residues	Length	Sheet
β-strand	15-16	2	81
β-strand	21-25	5	82
α-helix	26-27	2
α-helix	28-34	7
β-strand	43	1	83
β-strand	47-49	3	84
β-strand	51-52	2	84
β-strand	56	1	83
α-helix	81-85	5
β-strand	88	1	85
β-strand	94	1	86
α-helix	100-109	10
α-helix	124-132	9
α-helix	137-147	11
β-strand	192-194	3	87
β-strand	197-199	3	87
β-strand	215-216	2	87
α-helix	218-227	10
α-helix	230-235	6
α-helix	245-248	4
β-strand	250	1	86
β-strand	253	1	85
β-strand	264	1	88
β-strand	272	1	88
α-helix	273-274	2
α-helix	275-292	18
α-helix	293-297	5
α-helix	302-318	17
β-strand	329	1	89
β-strand	335	1	89
α-helix	339-342	4
α-helix	349-354	6
β-strand	357-358	2	90
β-strand	362-369	8	91
β-strand	377-380	4	91
α-helix	382-385	4
β-strand	389-393	5	92
α-helix	399-408	10
β-strand	416-420	5	92
β-strand	426-428	3	92
β-strand	445-449	5	92
α-helix	450	1
β-strand	455-459	5	91
α-helix	466-468	3
β-strand	471-476	6	91
β-strand	482-484	3	91
α-helix	486-488	3
α-helix	489-492	4
β-strand	500-504	5	91
α-helix	509-518	10
β-strand	520	1	91
α-helix	521-524	4
β-strand	526	1	93
β-strand	533	1	93
α-helix	540-548	9
β-strand	554-555	2	94
α-helix	557-563	7
α-helix	564-566	3
α-helix	574	1
β-strand	575	1	28
α-helix	576-577	2
β-strand	579-581	3	29
β-strand	585	1	29
β-strand	586-587	2	94
α-helix	588-595	8
β-strand	602-604	3	95
β-strand	628-631	4	95
β-strand	634-637	4	95
α-helix	642-645	4
α-helix	652-659	8
α-helix	662-683	22
β-strand	686	1	96
α-helix	689-691	3
α-helix	698-721	24
α-helix	725-728	4
α-helix	733-759	27
α-helix	765-771	7
α-helix	778-781	4
α-helix	782-786	5
β-strand	789-790	2	97
β-strand	793	1	98
β-strand	796	1	98
α-helix	798-799	2
β-strand	822-823	2	97
α-helix	833-868	36
β-strand	872-873	2	99
β-strand	879-880	2	99
β-strand	886-888	3	99
α-helix	891-893	3
β-strand	896	1	100
β-strand	902-905	4	101
α-helix	913-920	8
α-helix	927-933	7
β-strand	934	1	102
α-helix	936-944	9
α-helix	946-969	24
α-helix	971-973	3
β-strand	976-979	4	101
α-helix	983-993	11
β-strand	1002	1	102
α-helix	1006-1019	14
α-helix	1028-1037	10
α-helix	1039-1048	10
α-helix	1053-1056	4
α-helix	1062-1078	17
β-strand	1080	1	100
α-helix	1081-1082	2
α-helix	1087-1096	10
α-helix	1098-1100	3
α-helix	1121-1128	8
β-strand	1138-1142	5	103
β-strand	1143	1	104
α-helix	1146-1149	4
α-helix	1151-1161	11
β-strand	1164-1165	2	105
α-helix	1166-1169	4
β-strand	1170-1177	8	35
α-helix	1181-1183	3
α-helix	1190-1194	5
β-strand	1210-1216	7	35
α-helix	1218-1222	5
α-helix	1228-1239	12
β-strand	1243-1247	5	35
β-strand	1255-1261	7	35
α-helix	1281-1295	15
β-strand	1297-1299	3	105
β-strand	1306-1310	5	103
α-helix	1315-1317	3
β-strand	1319-1320	2	106
β-strand	1330-1331	2	106
β-strand	1335-1339	5	103
α-helix	1344-1347	4
β-strand	1352	1	104
β-strand	1358	1	103
α-helix	1362-1386	25
α-helix	1395-1404	10
α-helix	1416-1420	5
α-helix	1426-1431	6
α-helix	1435-1444	10
β-strand	1448-1449	2	82
α-helix	1454-1459	6
α-helix	1467-1469	3
β-strand	1472-1475	4	2
α-helix	1478-1481	4

Chain b: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	73
α-helix	50-75	26
β-strand	80-81	2	72
α-helix	83-93	11
β-strand	96-98	3	74

Chain B: 54 helices, 79 β-strands

Element	Residues	Length	Sheet
α-helix	22-36	15
α-helix	41-49	9
α-helix	50-54	5
α-helix	55-60	6
α-helix	63-65	3
β-strand	83-84	2	107
β-strand	87-93	7	107
β-strand	97	1	108
β-strand	107	1	108
α-helix	108-109	2
α-helix	110-115	6
β-strand	121-134	14	107
β-strand	138-153	16	107
α-helix	168-173	6
β-strand	185-187	3	109
β-strand	190-194	5	109
β-strand	196-200	5	110
α-helix	201	1
β-strand	205-208	4	111
β-strand	215-223	9	111
α-helix	231-232	2
β-strand	233-240	8	111
β-strand	256-258	3	111
β-strand	263	1	112
β-strand	267-268	2	111
α-helix	269-275	7
α-helix	281-288	8
α-helix	295-307	13
α-helix	314-323	10
β-strand	325	1	112
α-helix	332-341	10
α-helix	342-346	5
α-helix	349-351	3
α-helix	358-377	20
α-helix	381-384	4
α-helix	388-390	3
β-strand	391-394	4	110
α-helix	396-423	28
α-helix	440-450	11
β-strand	453	1	113
α-helix	459-461	3
β-strand	463	1	113
β-strand	467-469	3	109
α-helix	475-482	8
β-strand	484-486	3	110
α-helix	497-499	3
α-helix	503-505	3
β-strand	509	1	114
β-strand	523-525	3	110
β-strand	526	1	114
β-strand	531-532	2	115
α-helix	539-547	9
β-strand	551-552	2	116
α-helix	553-555	3
α-helix	558-561	4
β-strand	565-569	5	116
β-strand	572-577	6	116
α-helix	580-593	14
β-strand	602-606	5	116
β-strand	611-615	5	116
β-strand	621-627	7	115
β-strand	630	1	117
β-strand	632	1	117
α-helix	637-644	8
β-strand	646	1	118
β-strand	649	1	118
α-helix	653-658	6
β-strand	662-666	5	115
α-helix	670-672	3
β-strand	675-676	2	115
β-strand	695-696	2	115
α-helix	700-703	4
α-helix	714-716	3
β-strand	717	1	119
α-helix	719-728	10
β-strand	732	1	120
β-strand	748-751	4	47
β-strand	755	1	38
β-strand	759-760	2	121
α-helix	762-764	3
β-strand	776-782	7	122
β-strand	783	1	96
β-strand	794-797	4	122
α-helix	798-802	5
β-strand	808-817	10	47
β-strand	819	1	123
β-strand	827-829	3	123
β-strand	837-838	2	123
α-helix	845-847	3
β-strand	853	1	124
α-helix	854-855	2
β-strand	859	1	47
β-strand	865-867	3	124
β-strand	869-872	4	123
β-strand	889-891	3	123
β-strand	894-895	2	124
α-helix	896-897	2
β-strand	903-911	9	47
β-strand	917-927	11	47
β-strand	934-937	4	122
β-strand	943-949	7	122
β-strand	956	1	125
β-strand	965-967	3	122
α-helix	971-975	5
β-strand	977	1	119
α-helix	978-993	16
β-strand	997-998	2	121
α-helix	1008-1015	8
α-helix	1016-1018	3
β-strand	1025-1026	2	122
β-strand	1029	1	125
α-helix	1035	1
β-strand	1036	1	125
α-helix	1037	1
α-helix	1040	1
β-strand	1041-1050	10	122
β-strand	1051	1	120
α-helix	1055-1057	3
β-strand	1060	1	91
β-strand	1067	1	126
β-strand	1074	1	126
β-strand	1085-1086	2	90
α-helix	1088-1097	10
α-helix	1100-1104	5
α-helix	1105-1109	5
β-strand	1115-1119	5	81
β-strand	1126	1	81
β-strand	1127	1	127
α-helix	1128	1
β-strand	1136	1	127
β-strand	1146-1150	5	81
α-helix	1153-1163	11
β-strand	1167-1170	4	82

Chain c: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	28-35	8
β-strand	42-43	2	75
α-helix	47-72	26
β-strand	77-78	2	76
α-helix	80-88	9
α-helix	91-96	6
β-strand	101-102	2	77

Chain C: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	8-14	7	3
β-strand	18-24	7	3
α-helix	28-39	12
β-strand	44-55	12	4
α-helix	61-69	9
β-strand	73	1	5
α-helix	82-84	3
α-helix	85-87	3
β-strand	98-106	9	4
α-helix	112	1
β-strand	113-115	3	6
α-helix	117-119	3
β-strand	121-122	2	4
β-strand	129	1	5
β-strand	151-153	3	6
β-strand	158-168	11	4
α-helix	174-176	3
β-strand	179-182	4	3
β-strand	185-186	2	3
α-helix	200-202	3
α-helix	204-206	3
α-helix	218-220	3
β-strand	229-235	7	3
α-helix	241-268	28

Chain d: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	76
α-helix	56-83	28
β-strand	88-89	2	75
α-helix	91-101	11
α-helix	105-122	18

Chain D: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	1
α-helix	17-19	3
α-helix	24-27	4
α-helix	29	1
β-strand	30-31	2	2
α-helix	34-49	16
α-helix	55-58	4
α-helix	59-70	12
α-helix	78-88	11
α-helix	96-102	7
α-helix	108-114	7
α-helix	116-118	3
α-helix	124-137	14

24 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
RNA polymerase II subunit D	D	protein	142	Sus scrofa	A0A287ADR4 (AlphaFold model)
DNA-directed RNA polymerase II subunit E	E	protein	210	Sus scrofa	I3LSI7 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC2	F	protein	127	Sus scrofa	A0A8D1KNW4 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB7	G	protein	172	Sus scrofa	A0A4X1VKG7 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC3	H	protein	150	Sus scrofa	I3LCB2
DNA-directed RNA polymerase II subunit RPB9	I	protein	125	Sus scrofa	P60899
DNA-directed RNA polymerases I, II, and III subunit RPABC5	J	protein	67	Sus scrofa	A0A4X1VYD0
DNA-directed RNA polymerase II subunit RPB11-a	K	protein	117	Sus scrofa	F1RKE4
RNA polymerase II subunit K	L	protein	58	Sus scrofa	A0A8D0JYF1
RNA (46-mer)	P	RNA	46	synthetic construct
RNA polymerase-associated protein CTR9 homolog	Q	protein	1179	Homo sapiens	Q6PD62
Template DNA	T	DNA	197	synthetic construct

19 more molecules are not listed.

Sequence of entity 1 (D), FASTA

>9S0U_1 RNA polymerase II subunit D (chains D)
MAAGGSDPRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEV
FMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEG
RFEDEELQQILDDIQTKRSFQY

Sequence of entity 2 (E), FASTA

>9S0U_2 DNA-directed RNA polymerase II subunit E (chains E)
MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTV
LVAHNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVD
MAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVA
RYFGIKRGQVVKIIRPSETAGRYITYRLVQ

Sequence of entity 3 (F), FASTA

>9S0U_3 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKY
ERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGV
DELIISD

Sequence of entity 4 (G), FASTA

>9S0U_4 DNA-directed RNA polymerase II subunit RPB7 (chains G)
MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQ
PGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFD
PNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAIGSLMDDYLGLVS

Sequence of entity 5 (H), FASTA

>9S0U_5 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVI
ASTLYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGG
LLMRLQGDANNLHGFEVDSRVYLLMKKLAF

Sequence of entity 6 (I), FASTA

>9S0U_6 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MEPDGTYEPGFVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITH
EVDELTQIIADVSQDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCG
HRWTE

Sequence of entity 7 (J), FASTA

>9S0U_7 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL
NYAPLEK

Sequence of entity 8 (K), FASTA

>9S0U_8 DNA-directed RNA polymerase II subunit RPB11-a (chains K)
MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG
YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVAIKDKQEGIE

Sequence of entity 9 (L), FASTA

>9S0U_9 RNA polymerase II subunit K (chains L)
MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR

Sequence of entity 10 (P), FASTA

>9S0U_10 RNA (46-MER) (chains P)
UUAAGGAAUUAAGUCGUGCGUCUAAUAACCGGAGAGGGAACCCACU

Sequence of entity 11 (Q), FASTA

>9S0U_11 RNA polymerase-associated protein CTR9 homolog (chains Q)
MSRGSIEIPLRDTDEVIELDFDQLPEGDEVISILKQEHTQLHIWIALALEYYKQGKTEEF
VKLLEAARIDGNLDYRDHEKDQMTCLDTLAAYYVQQARKEKNKDNKKDLITQATLLYTMA
DKIIMYDQNHLLGRACFCLLEGDKMDQADAQFHFVLNQSPNNIPALLGKACISFNKKDYR
GALAYYKKALRTNPGCPAEVRLGMGHCFVKLNKLEKARLAFSRALELNSKCVGALVGLAV
LELNNKEADSIKNGVQLLSRAYTIDPSNPMVLNHLANHFFFKKDYSKVQHLALHAFHNTE
VEAMQAESCYQLARSFHVQEDYDQAFQYYYQATQFASSSFVLPFFGLGQMYIYRGDKENA
SQCFEKVLKAYPNNYETMKILGSLYAASEDQEKRDIAKGHLKKVTEQYPDDVEAWIELAQ
ILEQTDIQGALSAYGTATRILQEKVQADVPPEILNNVGALHFRLGNLGEAKKYFLASLDR
AKAEAEHDEHYYNAISVTTSYNLARLYEAMCEFHEAEKLYKNILREHPNYVDCYLRLGAM
ARDKGNFYEASDWFKEALQINQDHPDAWSLIGNLHLAKQEWGPGQKKFERILKQPSTQSD
TYSMLALGNVWLQTLHQPTRDREKEKRHQDRALAIYKQVLRNDAKNLYAANGIGAVLAHK
GYFREARDVFAQVREATADISDVWLNLAHIYVEQKQYISAVQMYENCLRKFYKHQNTEVV
LYLARALFKCGKLQECKQTLLKARHVAPSDTVLMFNVALVLQRLATSVLKDEKSNLKEVL
NAVKELELAHRYFSYLSKVGDKMRFDLALAATEARQCSDLLSQAQYHVARARKQDEEERE
LRAKQEQEKELLRQKLLKEQEEKRLREKEEQKKLLEQRAQYVEKTKNILMFTGETEATKE
KKRGGGGGRRSKKGGEFDEFVNDDTDDDLPISKKKKRRKGSGSEQEGEDEEGGERKKKKR
RRHPKGEEGSDDDETENGPKPKKRRPPKAEKKKAPKPERLPPSMKGKIKSKAIISSSDDS
SDEDKLKIADEGHPRNSNSNSDSDEDEQRKKCASSESDSDENQNKSGSEAGSPRRPRRQR
SDQDSDSDQPSRKRRPSGSEQSDNESVQSGRSHSGVSENDSRPASPSAESDHESERGSDN
EGSGQGSGNESEPEGSNNEASDRGSEHGSDDSDENLYFQ

Sequence of entity 12 (T), FASTA

>9S0U_12 Template DNA (chains T)
GCTCCCAGCTCCCTGCTGGCTCCGAGTGGGTTCTGCCGCGACAGTGATCGATATCAGAAT
CCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTA
CGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGT
CAGATATATACATCGAT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	9
MG	Magnesium ion	Mg	1

Primary citation

Molecular mechanism of co-transcriptional H3K36 methylation by SETD2. Walshe, J.L., Ochmann, M., Neef, U. et al. Nat Commun (2025) 16:9565-9565. DOI 10.1038/s41467-025-65439-y · PubMed

Other PDB entries of the same protein (UniProt A0A287ADR4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BZ0 1.9 Å, Structure of an STK19-containing TC-NER complex
7NVU 2.5 Å, RNA polymerase II core pre-initiation complex with open promoter DNA
7OOB 2.7 Å, Pol II-CSB-CSA-DDB1-UVSSA-ADPBeF3 (Structure2)
7F4G 2.78 Å, Structure of RPAP2-bound RNA polymerase II
7NVS 2.8 Å, RNA polymerase II core pre-initiation complex with closed promoter DNA in proximal…
7OO3 2.8 Å, Pol II-CSB-CSA-DDB1-UVSSA (Structure1)
8OEW 2.8 Å, Structure of the mammalian Pol II-Elongin complex, lacking the ELOA latch (composite…
8UHD 2.8 Å, Structure of paused transcription complex Pol II-DSIF-NELF - post-translocated
8OEV 2.86 Å, Structure of the mammalian Pol II-SPT6-Elongin complex, lacking ELOA latch (composite…
7NVT 2.9 Å, RNA polymerase II core pre-initiation complex with closed promoter DNA in distal position
7OOP 2.9 Å, Pol II-CSB-CSA-DDB1-UVSSA-PAF-SPT6 (Structure 3)
8S52 2.9 Å, RNA polymerase II core initially transcribing complex with an ordered RNA of 10 nt

Browse structure collections

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