29TK: DNA-directed RNA polymerase II subunit RPB3

Name: PDB 29TK: RNA polymerase II elongation complex with the +1 nucleosome
Published: 2026-07-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

RNA polymerase II elongation complex with the +1 nucleosome. Determined by electron microscopy at 3.9 Å resolution. Released 22 Jul 2026.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Sus scrofa, unidentified adenovirus, Homo sapiens
Chains: 26
Atoms: 49,023
Mol. weight: 941.24 kDa
Ligands: MG, ZN
Released: 22 Jul 2026

Explore 29TK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

29TK contains 228 α-helices and 280 β-strands across 23 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, 2 β-strands

Element	Residues	Length	Sheet
α-helix	42-43	2
α-helix	46-57	12
α-helix	65-79	15
β-strand	84-85	2	32
α-helix	87-114	28
β-strand	119-120	2	33
α-helix	122-131	10

Chain A: 74 helices, 69 β-strands

Element	Residues	Length	Sheet
α-helix	14	1
β-strand	15	1	42
β-strand	20-22	3	43
α-helix	28-34	7
β-strand	47	1	44
β-strand	52	1	44
α-helix	53	1
β-strand	86-94	9	45
α-helix	99-109	11
β-strand	110	1	46
α-helix	111	1
β-strand	117	1	46
α-helix	124-132	9
α-helix	137-149	13
β-strand	153	1	47
β-strand	187	1	47
α-helix	188-189	2
β-strand	190-194	5	48
β-strand	197-201	5	48
β-strand	214-215	2	48
α-helix	218-226	9
α-helix	230-234	5
α-helix	245-248	4
β-strand	250-255	6	45
β-strand	264	1	49
β-strand	272	1	49
α-helix	273-274	2
α-helix	275-295	21
α-helix	300-318	19
α-helix	326-328	3
β-strand	329	1	50
β-strand	335	1	50
α-helix	339-342	4
α-helix	350-355	6
β-strand	357-358	2	51
β-strand	362-369	8	52
β-strand	377-380	4	52
α-helix	382-387	6
β-strand	389-393	5	53
α-helix	399-408	10
β-strand	416-420	5	53
β-strand	426-428	3	53
β-strand	445-449	5	53
β-strand	455-459	5	52
α-helix	466-468	3
β-strand	469-476	8	52
β-strand	482-484	3	52
α-helix	486-489	4
β-strand	500-504	5	52
α-helix	509-518	10
β-strand	520	1	52
α-helix	521-524	4
β-strand	526	1	54
β-strand	533	1	54
α-helix	541-548	8
β-strand	554-555	2	55
α-helix	557-565	9
α-helix	574	1
β-strand	575	1	15
α-helix	576-577	2
β-strand	579-581	3	14
β-strand	585	1	14
β-strand	586-587	2	55
α-helix	588-595	8
β-strand	602-603	2	56
α-helix	612-615	4
β-strand	629-631	3	56
β-strand	634-637	4	56
α-helix	642-645	4
α-helix	652-659	8
α-helix	663-683	21
β-strand	686	1	57
α-helix	689-691	3
α-helix	696-721	26
α-helix	726-728	3
α-helix	733-758	26
α-helix	765-771	7
α-helix	778-781	4
α-helix	782-786	5
β-strand	789-790	2	58
β-strand	793	1	59
β-strand	796	1	59
α-helix	811	1
α-helix	818-820	3
β-strand	822-823	2	58
α-helix	833-866	34
β-strand	872-873	2	60
β-strand	879-880	2	60
β-strand	886-888	3	60
α-helix	891-893	3
β-strand	896	1	61
β-strand	902-905	4	62
α-helix	913-920	8
α-helix	928-933	6
β-strand	934	1	63
α-helix	936-943	8
α-helix	946-969	24
β-strand	976-979	4	62
α-helix	983-993	11
α-helix	1001	1
β-strand	1002	1	63
α-helix	1006-1017	12
α-helix	1028-1048	21
α-helix	1051-1053	3
α-helix	1054-1058	5
α-helix	1062-1078	17
β-strand	1080	1	61
α-helix	1081-1082	2
α-helix	1087-1096	10
α-helix	1097-1100	4
α-helix	1121-1128	8
β-strand	1138-1142	5	64
β-strand	1143	1	65
α-helix	1146-1149	4
α-helix	1151-1161	11
β-strand	1164	1	66
α-helix	1166-1169	4
β-strand	1170-1177	8	19
α-helix	1190-1196	7
β-strand	1210-1216	7	19
α-helix	1218-1224	7
α-helix	1228-1238	11
β-strand	1243-1246	4	19
β-strand	1255-1261	7	19
α-helix	1282-1294	13
β-strand	1299	1	66
β-strand	1307-1310	4	64
β-strand	1319-1321	3	67
β-strand	1329-1331	3	67
β-strand	1335-1339	5	64
α-helix	1343-1347	5
β-strand	1352	1	65
α-helix	1363-1368	6
α-helix	1371-1386	16
α-helix	1395-1404	10
β-strand	1408-1409	2	10
α-helix	1416-1419	4
α-helix	1426-1430	5
α-helix	1435-1445	11
β-strand	1448-1449	2	43
α-helix	1455-1459	5
β-strand	1471-1475	5	7
α-helix	1477-1480	4

Chain b: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	32-41	10
β-strand	46-47	2	33
α-helix	51-76	26
β-strand	81-82	2	32
α-helix	84-93	10
β-strand	97-99	3	34

Chain B: 49 helices, 86 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	63-64	2
β-strand	65-67	3	29
β-strand	83-87	5	29
β-strand	92-94	3	29
β-strand	97-99	3	68
β-strand	105-107	3	68
α-helix	108	1
α-helix	110-115	6
β-strand	121-133	13	29
β-strand	141-153	13	29
α-helix	168-173	6
β-strand	185-187	3	69
β-strand	190-193	4	69
β-strand	196-200	5	70
α-helix	201	1
β-strand	206-209	4	71
β-strand	217-220	4	71
β-strand	223	1	72
β-strand	233	1	72
β-strand	236-239	4	71
α-helix	249-252	4
β-strand	256-259	4	71
β-strand	263	1	73
β-strand	266-268	3	71
α-helix	269-275	7
α-helix	281-288	8
α-helix	297-307	11
α-helix	308-310	3
α-helix	314-322	9
β-strand	325	1	73
α-helix	332-344	13
α-helix	349-351	3
α-helix	358-377	20
α-helix	382-384	3
β-strand	391-394	4	70
α-helix	396-424	29
α-helix	437-449	13
β-strand	453	1	74
β-strand	463	1	74
β-strand	468-469	2	69
α-helix	470-471	2
α-helix	475-482	8
β-strand	484-486	3	70
α-helix	501-502	2
β-strand	509	1	75
β-strand	523-525	3	70
β-strand	526	1	75
β-strand	531-532	2	76
α-helix	539-547	9
β-strand	551-552	2	77
β-strand	565-569	5	77
β-strand	572-577	6	77
α-helix	580-592	13
β-strand	602-606	5	77
β-strand	611-615	5	77
β-strand	621-626	6	76
β-strand	628-629	2	78
β-strand	632-633	2	78
α-helix	637-644	8
α-helix	653-657	5
β-strand	662-666	5	76
α-helix	669-671	3
β-strand	675-676	2	79
α-helix	679-683	5
β-strand	695-696	2	79
α-helix	700-703	4
α-helix	706-709	4
β-strand	717	1	80
α-helix	719-728	10
α-helix	729-731	3
β-strand	732	1	81
β-strand	748-751	4	25
β-strand	755	1	22
β-strand	759-760	2	82
β-strand	776-779	4	83
β-strand	780-782	3	84
β-strand	783	1	57
β-strand	794-797	4	84
α-helix	798-802	5
β-strand	808-817	10	25
β-strand	827-829	3	85
α-helix	831-833	3
β-strand	837	1	85
α-helix	845-847	3
β-strand	848	1	86
β-strand	853	1	87
β-strand	854	1	86
α-helix	855	1
β-strand	859	1	25
β-strand	864-867	4	87
β-strand	869-872	4	85
α-helix	873	1
β-strand	889-891	3	85
β-strand	894-896	3	87
α-helix	897	1
β-strand	903-904	2	25
β-strand	908-911	4	25
β-strand	917-927	11	25
β-strand	934-936	3	88
β-strand	943-944	2	88
β-strand	945-949	5	84
β-strand	956	1	84
β-strand	965-967	3	84
α-helix	969-971	3
β-strand	977	1	80
α-helix	978-993	16
α-helix	996	1
β-strand	997-998	2	82
α-helix	1008-1016	9
β-strand	1025-1029	5	84
α-helix	1035	1
β-strand	1036-1042	7	84
β-strand	1045-1048	4	83
β-strand	1049-1050	2	88
β-strand	1051	1	81
β-strand	1060-1061	2	52
β-strand	1067	1	89
β-strand	1074	1	89
β-strand	1085-1086	2	51
α-helix	1088-1097	10
α-helix	1100-1104	5
α-helix	1105-1109	5
β-strand	1115-1119	5	42
β-strand	1125	1	42
β-strand	1127-1129	3	90
β-strand	1134-1136	3	90
β-strand	1137	1	91
β-strand	1142	1	91
β-strand	1146-1150	5	42
α-helix	1153-1164	12
β-strand	1170-1172	3	43

Chain c: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-22	5
α-helix	28-37	10
β-strand	43-44	2	35
α-helix	47-73	27
β-strand	78-79	2	36
α-helix	81-90	10
α-helix	92-97	6
β-strand	101-103	3	37
α-helix	114-116	3

Chain C: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	8-14	7	1
β-strand	19-24	6	1
α-helix	28-40	13
β-strand	44-55	12	2
α-helix	61-69	9
β-strand	73	1	3
α-helix	83-84	2
β-strand	99-106	8	2
α-helix	112	1
β-strand	113-116	4	4
α-helix	117-119	3
β-strand	121-122	2	2
β-strand	129	1	3
β-strand	149-153	5	4
β-strand	158-168	11	2
α-helix	174-176	3
β-strand	179	1	5
β-strand	184-186	3	1
α-helix	200-202	3
α-helix	204-206	3
α-helix	218-220	3
β-strand	229-231	3	1
β-strand	233	1	1
β-strand	235	1	5
α-helix	243-270	28

Chain d: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	39-49	11
β-strand	54-55	2	36
α-helix	57-84	28
β-strand	89-90	2	35
α-helix	92-102	11
α-helix	106-124	19

Chain D: 10 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	6
α-helix	17-19	3
β-strand	21	1	6
β-strand	30	1	7
α-helix	34-49	16
α-helix	55-58	4
α-helix	59-70	12
α-helix	77-89	13
α-helix	94-103	10
α-helix	108-114	7
α-helix	116-118	3
α-helix	124-137	14
α-helix	138-140	3

15 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 RPB3	C	protein	275	Sus scrofa	I3LCH3 (AlphaFold model)
RNA polymerase II subunit D	D	protein	184	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 subunit	G	protein	171	Sus scrofa	A0A4X1VKG7
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 (5'-r(papcpapcpcpcpapgpcpc)-3')	P	RNA	10	unidentified adenovirus
General transcription factor IIF subunit 1	Q	protein	517	Homo sapiens	P35269

10 more molecules are not listed.

Sequence of entity 1 (C), FASTA

>29TK_1 DNA-directed RNA polymerase II subunit RPB3 (chains C)
MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH
DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL
ISNSPRVIPVTSRNRDNDPSDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR
PETIVLSALSGLKKKLSDLQTQLSHEIQSDVLTIN

Sequence of entity 2 (D), FASTA

>29TK_2 RNA polymerase II subunit D (chains D)
MWGPAQPYSDSALSPKPRPFRAVFRGSALPFPAVRVEVRGRSMAAGGSDPRAGDVEEDAS
QLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRE
TIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDIQTKR
SFQY

Sequence of entity 3 (E), FASTA

>29TK_3 DNA-directed RNA polymerase II subunit E (chains E)
MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTV
LVAHNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVD
MAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVA
RYFGIKRGQVVKIIRPSETAGRYITYRLVQ

Sequence of entity 4 (F), FASTA

>29TK_4 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKY
ERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGV
DELIISD

Sequence of entity 5 (G), FASTA

>29TK_5 DNA-directed RNA polymerase subunit (chains G)
MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQ
PGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFD
PNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAIGSLMDDYLGLV

Sequence of entity 6 (H), FASTA

>29TK_6 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVI
ASTLYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGG
LLMRLQGDANNLHGFEVDSRVYLLMKKLAF

Sequence of entity 7 (I), FASTA

>29TK_7 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MEPDGTYEPGFVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITH
EVDELTQIIADVSQDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCG
HRWTE

Sequence of entity 8 (J), FASTA

>29TK_8 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL
NYAPLEK

Sequence of entity 9 (K), FASTA

>29TK_9 DNA-directed RNA polymerase II subunit RPB11-a (chains K)
MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG
YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVAIKDKQEGIE

Sequence of entity 10 (L), FASTA

>29TK_10 RNA polymerase II subunit K (chains L)
MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR

Sequence of entity 11 (P), FASTA

>29TK_11 RNA (5'-R(P*AP*CP*AP*CP*CP*CP*AP*GP*CP*C)-3') (chains P)
ACACCCAGCC

Sequence of entity 12 (Q), FASTA

>29TK_12 General transcription factor IIF subunit 1 (chains Q)
MAALGPSSQNVTEYVVRVPKNTTKKYNIMAFNAADKVNFATWNQARLERDLSNKKIYQEE
EMPESGAGSEFNRKLREEARRKKYGIVLKEFRPEDQPWLLRVNGKSGRKFKGIKKGGVTE
NTSYYIFTQCPDGAFEAFPVHNWYNFTPLARHRTLTAEEAEEEWERRNKVLNHFSIMQQR
RLKDQDQDEDEEEKEKRGRRKASELRIHDLEDDLEMSSDASDASGEEGGRVPKAKKKAPL
AKGGRKKKKKKGSDDEAFEDSDDGDFEGQEVDYMSDGSSSSQEEPESKAKAPQQEEGPKG
VDEQSDSSEESEEEKPPEEDKEEEEEKKAPTPQEKKRRKDSSEESDSSEESDIDSEASSA
LFMAKKKTPPKRERKPSGGSSRGNSRPGTPSAEGGSTSSTLRAAASKLEQGKRVSEMPAA
KRLRLDTGPQSLSGKSTPQPPSGKTTPNSGDVQVTEDAVRRYLTRKPMTTKDLLKKFQTK
KTGLSSEQTVNVLAQILKRLNPERKMINDKMHFSLKE

Ligands and cofactors

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

Primary citation

The +1 nucleosome functions in RNA Pol II transcription initiation and the transition to elongation. Zhan, Y., Abril-Garrido, J., Grabbe, F. et al. Mol Cell (2026) 86:2939. DOI 10.1016/j.molcel.2026.06.042 · PubMed

Other PDB entries of the same protein (UniProt I3LCH3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BZ0 1.9 Å, Structure of an STK19-containing TC-NER complex
9HVQ 2.0 Å, Structure of the transcribing Pol II-DSIF-PAF-SPT6-RECQL5 complex
7NVU 2.5 Å, RNA polymerase II core pre-initiation complex with open promoter DNA
8QEP 2.5 Å, RNA polymerase II bound to Alu RNA right arm
8B3D 2.6 Å, Structure of the Pol II-TCR-ELOF1 complex.
7OOB 2.7 Å, Pol II-CSB-CSA-DDB1-UVSSA-ADPBeF3 (Structure2)
8UHG 2.7 Å, Structure of paused transcription complex Pol II-DSIF-NELF - poised post-translocated
8UI0 2.7 Å, Structure of poised transcription complex Pol II-DSIF-NELF - pre-translocated
8WAV 2.72 Å, De novo transcribing complex 12 (TC12), the early elongation complex with Pol II…
8WAX 2.75 Å, De novo transcribing complex 14 (TC14), the early elongation complex with Pol II…
8WAZ 2.76 Å, De novo transcribing complex 16 (TC16), the early elongation complex with Pol II…
7F4G 2.78 Å, Structure of RPAP2-bound RNA polymerase II

Browse structure collections

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