9J0N: DNA-directed RNA polymerase subunit

Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc). Determined by electron microscopy at 3.4 Å resolution. Released 5 Feb 2025.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Sus scrofa, Homo sapiens
Chains: 30
Atoms: 59,666
Mol. weight: 1171.17 kDa
Ligands: MG, ZN
Released: 5 Feb 2025

Explore 9J0N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9J0N contains 319 α-helices and 291 β-strands across 27 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.

Chains a and e: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	85
α-helix	86-113	28
β-strand	118-119	2	86
α-helix	121-131	11

Chain A: 67 helices, 68 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	1
β-strand	20-25	6	2
α-helix	26-27	2
α-helix	28-34	7
β-strand	47	1	3
β-strand	52	1	3
α-helix	53	1
β-strand	86-94	9	4
α-helix	100-109	10
β-strand	110	1	5
β-strand	117	1	5
α-helix	124-132	9
α-helix	137-148	12
β-strand	190-194	5	6
β-strand	197-201	5	6
β-strand	214	1	6
α-helix	218-226	9
α-helix	230-236	7
β-strand	239	1	7
β-strand	243	1	7
α-helix	245-247	3
β-strand	250-255	6	4
α-helix	256	1
β-strand	264	1	8
β-strand	272	1	8
α-helix	275-296	22
α-helix	302-318	17
β-strand	329-330	2	9
β-strand	334-335	2	9
α-helix	336-337	2
α-helix	339-342	4
α-helix	349	1
α-helix	350-354	5
β-strand	357-358	2	10
β-strand	362-369	8	11
β-strand	377-380	4	11
α-helix	382-385	4
β-strand	389-393	5	12
α-helix	399-408	10
β-strand	416-420	5	12
β-strand	426-428	3	12
β-strand	445-449	5	12
β-strand	455-459	5	11
α-helix	466-468	3
β-strand	469-476	8	11
β-strand	482-484	3	11
α-helix	489-492	4
β-strand	500-504	5	11
α-helix	509-518	10
β-strand	520	1	11
α-helix	521-524	4
β-strand	526-527	2	13
β-strand	532-533	2	13
α-helix	539-548	10
β-strand	554-555	2	14
α-helix	557-564	8
α-helix	574	1
β-strand	575	1	15
α-helix	576-577	2
β-strand	579	1	16
β-strand	585	1	16
β-strand	586-587	2	14
α-helix	588-592	5
β-strand	602-603	2	17
β-strand	629-631	3	17
β-strand	634-637	4	17
α-helix	642-645	4
α-helix	652-659	8
α-helix	662-683	22
β-strand	686	1	18
α-helix	689-692	4
α-helix	698-721	24
α-helix	726-728	3
α-helix	733-759	27
α-helix	765-771	7
α-helix	778-785	8
β-strand	789-790	2	19
β-strand	793	1	20
β-strand	796	1	20
β-strand	822-823	2	19
α-helix	833-867	35
β-strand	872-873	2	21
β-strand	879-880	2	21
β-strand	886-888	3	21
α-helix	891-893	3
β-strand	896	1	22
β-strand	902-905	4	23
α-helix	913-920	8
α-helix	927-933	7
β-strand	934	1	24
α-helix	936-944	9
α-helix	946-969	24
α-helix	971-973	3
β-strand	976-979	4	23
α-helix	983-994	12
β-strand	1002	1	24
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	22
α-helix	1087-1096	10
α-helix	1097-1100	4
α-helix	1121-1128	8
β-strand	1140-1142	3	25
β-strand	1143	1	26
α-helix	1146-1148	3
α-helix	1152-1161	10
β-strand	1164	1	27
α-helix	1166-1168	3
β-strand	1170-1176	7	28
α-helix	1190-1194	5
β-strand	1211-1216	6	28
α-helix	1218-1223	6
α-helix	1228-1239	12
β-strand	1243-1247	5	28
β-strand	1255-1261	7	28
α-helix	1281-1292	12
β-strand	1299	1	27
β-strand	1308-1310	3	25
β-strand	1319	1	29
β-strand	1331	1	29
β-strand	1335-1337	3	25
β-strand	1352	1	26
α-helix	1362-1369	8
α-helix	1372-1386	15
α-helix	1395-1405	11
α-helix	1416-1419	4
α-helix	1426-1430	5
α-helix	1435-1444	10
β-strand	1448-1449	2	2
α-helix	1454-1459	6
β-strand	1471-1475	5	30
α-helix	1479-1481	3

Chain b: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	31-41	11
β-strand	45-46	2	86
α-helix	50-75	26
β-strand	80-81	2	85
α-helix	83-93	11
β-strand	96-97	2	87

Chain B: 49 helices, 76 β-strands

Element	Residues	Length	Sheet
α-helix	22-36	15
α-helix	41-49	9
α-helix	50-54	5
α-helix	55-61	7
α-helix	63-64	2
β-strand	83-84	2	32
β-strand	87-93	7	32
β-strand	97-98	2	33
β-strand	106-107	2	33
α-helix	110-115	6
β-strand	121-134	14	32
β-strand	138-153	16	32
β-strand	155	1	34
α-helix	168-173	6
β-strand	185-187	3	34
β-strand	190-194	5	34
α-helix	195-196	2
β-strand	197-200	4	35
β-strand	206-208	3	36
β-strand	215-220	6	36
β-strand	221	1	37
β-strand	235	1	37
β-strand	236-240	5	36
β-strand	256-259	4	36
β-strand	263	1	38
β-strand	267-268	2	36
α-helix	269-275	7
α-helix	281-288	8
α-helix	295-299	5
α-helix	303-306	4
α-helix	314-322	9
β-strand	325	1	38
α-helix	332-345	14
α-helix	358-377	20
α-helix	381-383	3
α-helix	388-390	3
β-strand	391-394	4	35
α-helix	396-423	28
α-helix	431-434	4
α-helix	437-450	14
β-strand	453	1	39
α-helix	459-461	3
β-strand	463	1	39
β-strand	467-469	3	34
α-helix	475-482	8
β-strand	484	1	40
β-strand	509	1	41
β-strand	525	1	40
β-strand	526	1	41
β-strand	531-532	2	42
α-helix	539-547	9
α-helix	550	1
β-strand	551	1	43
α-helix	552	1
α-helix	558-560	3
β-strand	565-569	5	43
β-strand	572-577	6	43
α-helix	580-593	14
β-strand	602-606	5	43
β-strand	611-615	5	43
β-strand	621-627	7	42
β-strand	628	1	44
β-strand	633	1	44
α-helix	637-644	8
α-helix	653-658	6
β-strand	662-666	5	42
α-helix	667-670	4
β-strand	675-676	2	42
α-helix	679-682	4
β-strand	695-696	2	42
α-helix	700-703	4
α-helix	707-709	3
α-helix	714-716	3
α-helix	719-728	10
β-strand	732	1	45
β-strand	748-751	4	46
β-strand	755	1	47
β-strand	759-760	2	48
α-helix	762-765	4
β-strand	776-782	7	49
β-strand	783	1	18
β-strand	793-797	5	49
α-helix	798-802	5
β-strand	808-817	10	46
β-strand	820-822	3	50
β-strand	825-826	2	50
β-strand	827-829	3	51
β-strand	853	1	52
α-helix	854-855	2
β-strand	859	1	46
β-strand	865-867	3	52
β-strand	869-872	4	51
β-strand	889-891	3	51
β-strand	894-895	2	52
α-helix	896-897	2
β-strand	903-911	9	46
β-strand	917-927	11	46
β-strand	934-936	3	49
β-strand	942-949	8	49
β-strand	956	1	53
β-strand	965-967	3	49
α-helix	971-975	5
α-helix	978-993	16
β-strand	997-998	2	48
α-helix	1008-1016	9
β-strand	1025-1026	2	49
β-strand	1029	1	53
β-strand	1036	1	53
α-helix	1040	1
β-strand	1041-1050	10	49
β-strand	1051	1	45
α-helix	1055-1057	3
β-strand	1060-1062	3	11
β-strand	1085-1086	2	10
α-helix	1088-1097	10
α-helix	1100-1104	5
α-helix	1105-1109	5
β-strand	1115-1119	5	1
β-strand	1125	1	1
α-helix	1126	1
β-strand	1127	1	54
β-strand	1136	1	54
β-strand	1146-1150	5	1
α-helix	1153-1164	12
β-strand	1167-1172	6	2

Chain c: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	88
α-helix	46-72	27
β-strand	77-78	2	89
α-helix	79	1
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	90

Chain C: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	8-14	7	55
β-strand	18-24	7	55
α-helix	28-39	12
β-strand	44-55	12	56
α-helix	61-69	9
β-strand	73	1	57
α-helix	83-84	2
β-strand	99-106	8	56
β-strand	113-116	4	58
α-helix	117-119	3
β-strand	121-122	2	56
β-strand	129	1	57
α-helix	147-148	2
β-strand	149-153	5	58
β-strand	158-168	11	56
α-helix	174-176	3
β-strand	179-185	7	55
α-helix	200-202	3
α-helix	204-206	3
α-helix	218-220	3
β-strand	229-235	7	55
α-helix	241-267	27

Chain d: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	29-32	4
α-helix	35-45	11
β-strand	50-51	2	89
α-helix	53-80	28
β-strand	85-86	2	88
α-helix	88-98	11
α-helix	102-120	19

Chain D: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	64
α-helix	24-27	4
β-strand	30-31	2	30
α-helix	34-50	17
α-helix	55-58	4
α-helix	59-70	12
α-helix	77-89	13
α-helix	96-101	6
α-helix	108-114	7
α-helix	116-118	3
α-helix	124-137	14

18 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 subunit	A	protein	1970	Sus scrofa	A0A8D1DPV6
DNA-directed RNA polymerase subunit beta	B	protein	1174	Sus scrofa	A0A0B8RVL1 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB3	C	protein	271	Sus scrofa	I3LCH3 (AlphaFold model)
DNA-directed RNA polymerase II subunit E	E	protein	210	Sus scrofa	I3LSI7 (AlphaFold model)
DNA-directed RNA polymerase II subunit F	F	protein	127	Sus scrofa	A0A4X1VEK9
DNA-directed RNA polymerase II subunit RPB7	G	protein	172	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
Transcription elongation factor SPT4	Y	protein	118	Homo sapiens	P63272
Transcription elongation factor SPT5	Z	protein	1107	Homo sapiens	O00267
Non-template DNA (157-MER)	N	DNA	198	Homo sapiens
RNA (5'-r(pupgpgpgpupgpgpupgpgpcpc)-3')	P	RNA	42	Homo sapiens

14 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>9J0N_1 DNA-directed RNA polymerase subunit (chains A)
MHGGGPPSGDSACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDP
RQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVD
SNNPKIKDILAKSKGQPKKRLTHVYDLCKGKNICEGGEEMDNKFGVEQPEGDEDLTKEKG
HGGCGRYQPRIRRSGLELYAEWKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEP
RYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAA
HVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVD
FSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYII
RDNGDRIDLRFHPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWS
TFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQD
TLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQPAILKPRPLWTGKQIFSLIIPGHI
NCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEM
GHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKA
HNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKIN
ISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHA
MGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLAGES
VEFQNLATLKPSNKAFEKKFRFDYTNERALRRTLQEDLVKDVLSNAHIQNELEREFERMR
EDREVLRVIFPTGDSKVVLPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKL
VIVNGDDPLSRQAQENATLLFNIHLRSTLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAI
AHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLT
VFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMP
DFDVARISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIR
IMNSDENKMQEEEEVVDKMDDDVFLRCIESNMLTDMTLQGIEQISKVYMHLPQTDNKKKI
IITEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALER
ELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLM
EAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAEKCKYGMEIPTNIPGLGAAGPTG
MFFGSAPSPMGGISPAMTPWNQGATPAYGAWSPSVGSGMTPGAAGFSPSAASDASGFSPG
YSPAWSPTPGSPGSPGPSSPYIPSPGGAMSPSYSPTSPAYEPRSPGGYTPQSPSYSPTSP
SYSPTSPSYSPTSPNYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP
TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS
YSPTSPNYSPTSPNYTPTSPSYSPTSPSYSPTSPNYTPTSPNYSPTSPSYSPTSPSYSPT
SPSYSPSSPRYTPQSPTYTPSSPSYSPSSPSYSPTSPKYTPTSPSYSPSSPEYTPTSPKY
SPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTS
PKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSDEEN

Sequence of entity 2 (B), FASTA

>9J0N_2 DNA-directed RNA polymerase subunit beta (chains B)
MYDADEDMQYDEDDDEITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVE
DAPPIDLQAEAQHASGEVEEPPRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTY
SAPLYVDITKTVIKEGEEQLQTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLD
PGGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKYAYTGECRSCLENSSRPTSTIWVSML
ARGGQGAKKSAIGQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEM
VKPSLDEAFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCETK
KAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQ
KFIDRGKDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLS
HLRRLNSPIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSP
ILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSE
VSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNNYSWQDLVASG
VVEYIDTLEEETVMLAMTPDDLQEKEVAYCSTYTHCEIHPSMILGVCASIIPFPDHNQSP
RNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIV
AIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGM
RHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELEGTNRRYTKRDCSTFLRTSE
TGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEG
ITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDAVNVQKISNLLSDYGY
HLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSR
DGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANTRTHTYECRGC
RNKTQISLVRMPYACKLLFQELMSMSIAPRMMSV

Sequence of entity 3 (C), FASTA

>9J0N_3 DNA-directed RNA polymerase II subunit RPB3 (chains C)
MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH
DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL
ISNSPRVIPVTSRNRDNDPSDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR
PETIVLSALSGLKKKLSDLQTQLSHEIQSDV

Sequence of entity 4 (E), FASTA

>9J0N_4 DNA-directed RNA polymerase II subunit E (chains E)
MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTV
LVAHNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVD
MAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVA
RYFGIKRGQVVKIIRPSETAGRYITYRLVQ

Sequence of entity 5 (F), FASTA

>9J0N_5 DNA-directed RNA polymerase II subunit F (chains F)
MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKY
ERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGV
DELIISD

Sequence of entity 6 (G), FASTA

>9J0N_6 DNA-directed RNA polymerase II subunit RPB7 (chains G)
MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQ
PGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFD
PNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAIGSLMDDYLGLVS

Sequence of entity 7 (H), FASTA

>9J0N_7 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVI
ASTLYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGG
LLMRLQGDANNLHGFEVDSRVYLLMKKLAF

Sequence of entity 8 (I), FASTA

>9J0N_8 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MEPDGTYEPGFVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITH
EVDELTQIIADVSQDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCG
HRWTE

Sequence of entity 9 (Y), FASTA

>9J0N_9 Transcription elongation factor SPT4 (chains Y)
SMALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDG
IIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGVAYKSRDTAIKT

Sequence of entity 10 (Z), FASTA

>9J0N_10 Transcription elongation factor SPT5 (chains Z)
MSDSEDSNFSEEEDSERSSDGEEAEVDEERRSAAGSEKEEEPEDEEEEEEEEEYDEEEEE
EDDDRPPKKPRHGGFILDEADVDDEYEDEDQWEDGAEDILEKEEIEASNIDNVVLDEDRS
GARRLQNLWRDQREEELGEYYMKKYAKSSVGETVYGGSDELSDDITQQQLLPGVKDPNLW
TVKCKIGEERATAISLMRKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIE
GVGNLRLGYWNQQMVPIKEMTDVLKVVKEVANLKPKSWVRLKRGIYKDDIAQVDYVEPSQ
NTISLKMIPRIDYDRIKARMSLKDWFAKRKKFKRPPQRLFDAEKIRSLGGDVASDGDFLI
FEGNRYSRKGFLFKSFAMSAVITEGVKPTLSELEKFEDQPEGIDLEVVTESTGKEREHNF
QPGDNVEVCEGELINLQGKILSVDGNKITIMPKHEDLKDMLEFPAQELRKYFKMGDHVKV
IAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLCSETASGVDVGGQHEWGELV
QLDPQTVGVIVRLERETFQVLNMYGKVVTVRHQAVTRKKDNRFAVALDSEQNNIHVKDIV
KVIDGPHSGREGEIRHLFRSFAFLHCKKLVENGGMFVCKTRHLVLAGGSKPRDVTNFTVG
GFAPMSPRISSPMHPSAGGQRGGFGSPGGGSGGMSRGRGRRDNELIGQTVRISQGPYKGY
IGVVKDATESTARVELHSTCQTISVDRQRLTTVGSRRPGGMTSTYGRTPMYGSQTPMYGS
GSRTPMYGSQTPLQDGSRTPHYGSQTPLHDGSRTPAQSGAWDPNNPNTPSRAEEEYEYAF
DDEPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQG
SYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAPSP
GGYNPHTPGSGIEQNSSDWVTTDIQVKVRDTYLDTQVVGQTGVIRSVTGGMCSVYLKDSE
KVVSISSEHLEPITPTKNNKVKVILGEDREATGVLLSIDGEDGIVRMDLDEQLKILNLRF
LGKLLEAKETAAAKFERQHMDSSTSAA

Sequence of entity 11 (N), FASTA

>9J0N_11 Non-template DNA (157-MER) (chains N)
GCTTACGTCAGTCTGGCCATCTTTGTGTTTGGTGTGTTTGGGTGGTGGCCGTTTTCGTTG
TTTTTTTCTGTCTCGTGCCTGGTGTCTTGGGTGTAATCCCCTTGGCGGTTAAAACGCGGG
GGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCT
CGGCACCGGGATTCTGAT

Sequence of entity 12 (P), FASTA

>9J0N_12 RNA (5'-R(P*UP*GP*GP*GP*UP*GP*GP*UP*GP*GP*CP*C)-3') (chains P)
AAUUAGCUCUUGUGUUGUGUUUGGUGUGUUUGGGUGGUGGCC

Ligands and cofactors

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

Primary citation

Structural insights into promoter-proximal pausing of RNA polymerase II at +1 nucleosome. Naganuma, M., Kujirai, T., Ehara, H. et al. Sci Adv (2025) 11:eadu0577-eadu0577. DOI 10.1126/sciadv.adu0577 · PubMed

Other PDB entries of the same protein (UniProt A0A8D1DPV6), best resolution first:

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
8WAU 2.78 Å, De novo transcribing complex 11 (TC11), the early elongation complex with Pol II…

Browse structure collections

About this viewer

MolViewer shows 9J0N directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.