8QEQ: RNA polymerase II

Name: PDB 8QEQ: RNA polymerase II bound to minimal Alu RNA right arm in the alternative conformation
Published: 2024-12-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

RNA polymerase II bound to minimal Alu RNA right arm in the alternative conformation. Determined by electron microscopy at 3.1 Å resolution. Released 11 Dec 2024.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Sus scrofa domesticus, Homo sapiens
Chains: 11
Atoms: 29,242
Mol. weight: 506.99 kDa
Ligands: MG, ZN
Released: 11 Dec 2024

Explore 8QEQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8QEQ contains 187 α-helices and 218 β-strands across 10 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: 82 helices, 73 β-strands

Element	Residues	Length	Sheet
α-helix	14	1
β-strand	15	1	1
β-strand	20-22	3	2
β-strand	25	1	3
α-helix	28-34	7
β-strand	47	1	4
β-strand	52	1	4
α-helix	53	1
β-strand	86-95	10	5
α-helix	100-107	8
β-strand	110	1	6
β-strand	117	1	6
α-helix	124-132	9
α-helix	137-148	12
β-strand	153	1	7
α-helix	186	1
β-strand	187	1	7
α-helix	188-189	2
β-strand	190-194	5	8
β-strand	197-201	5	8
β-strand	213-215	3	8
α-helix	218-226	9
α-helix	240-243	4
α-helix	245-248	4
β-strand	249-255	7	5
α-helix	258-260	3
β-strand	263	1	9
β-strand	273	1	9
α-helix	275-292	18
α-helix	293-297	5
α-helix	300-318	19
α-helix	326-328	3
β-strand	329	1	10
β-strand	335	1	10
α-helix	336	1
α-helix	349-354	6
β-strand	357-359	3	11
β-strand	362-369	8	12
β-strand	377-381	5	12
α-helix	382-387	6
β-strand	389-393	5	13
α-helix	399-408	10
β-strand	416-420	5	13
β-strand	426-428	3	13
α-helix	435-437	3
β-strand	445-449	5	13
α-helix	450-451	2
β-strand	455-459	5	12
α-helix	466-468	3
β-strand	469-477	9	12
β-strand	482-484	3	12
α-helix	486-488	3
α-helix	489-492	4
β-strand	500-504	5	12
α-helix	509-514	6
α-helix	515-519	5
β-strand	520	1	12
α-helix	521-524	4
β-strand	526	1	14
β-strand	533	1	14
α-helix	540-548	9
β-strand	554-555	2	15
α-helix	557-563	7
α-helix	573-574	2
β-strand	575	1	16
α-helix	576-577	2
β-strand	579-581	3	17
β-strand	585	1	17
β-strand	586-587	2	15
α-helix	588-595	8
β-strand	602-605	4	18
β-strand	627-631	5	18
β-strand	634-637	4	18
α-helix	642-645	4
α-helix	652-660	9
α-helix	662-683	22
α-helix	689-692	4
α-helix	696-721	26
α-helix	727-728	2
α-helix	733-758	26
α-helix	765-772	8
α-helix	778-785	8
β-strand	789-790	2	19
β-strand	792-793	2	20
β-strand	796-797	2	20
α-helix	798-799	2
β-strand	802	1	21
β-strand	805	1	21
α-helix	811	1
β-strand	822-823	2	19
α-helix	833-854	22
α-helix	859-868	10
β-strand	872-873	2	22
β-strand	879-880	2	22
β-strand	886-888	3	22
α-helix	891-893	3
β-strand	896	1	23
β-strand	902-905	4	24
α-helix	913-920	8
α-helix	927-933	7
β-strand	934	1	25
α-helix	936-943	8
α-helix	946-969	24
β-strand	976-979	4	24
α-helix	983-993	11
α-helix	1001	1
β-strand	1002	1	25
α-helix	1006-1017	12
α-helix	1028-1037	10
α-helix	1039-1048	10
α-helix	1053-1056	4
α-helix	1062-1077	16
β-strand	1080	1	23
α-helix	1081-1082	2
α-helix	1087-1096	10
α-helix	1097-1100	4
α-helix	1120-1129	10
β-strand	1139-1142	4	26
β-strand	1143	1	27
α-helix	1146-1148	3
α-helix	1151-1161	11
β-strand	1162	1	28
β-strand	1164	1	29
α-helix	1166-1169	4
β-strand	1170-1177	8	30
α-helix	1181-1183	3
α-helix	1190-1193	4
α-helix	1195-1198	4
β-strand	1210-1216	7	30
α-helix	1218-1224	7
α-helix	1228-1239	12
β-strand	1243-1247	5	30
β-strand	1256-1261	6	30
α-helix	1263-1266	4
α-helix	1281-1295	15
β-strand	1299	1	29
β-strand	1301	1	28
β-strand	1306-1310	5	26
β-strand	1319-1322	4	31
β-strand	1328-1331	4	31
β-strand	1335-1339	5	26
α-helix	1343-1348	6
β-strand	1352	1	27
β-strand	1358-1359	2	26
α-helix	1362-1368	7
α-helix	1371-1387	17
α-helix	1395-1404	10
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
α-helix	1467-1469	3
β-strand	1472-1475	4	32
α-helix	1479-1481	3

Chain B: 59 helices, 83 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	65-67	3	33
β-strand	84-93	10	33
β-strand	97-99	3	34
β-strand	105-107	3	34
α-helix	110-116	7
β-strand	121-132	12	33
β-strand	140-153	14	33
α-helix	154-155	2
α-helix	168-173	6
β-strand	185-187	3	35
β-strand	190-193	4	35
α-helix	195	1
β-strand	196-200	5	36
α-helix	201	1
β-strand	205-208	4	37
β-strand	215-223	9	37
α-helix	231-232	2
β-strand	233-240	8	37
α-helix	247-252	6
α-helix	254-255	2
β-strand	256-259	4	37
β-strand	263	1	38
β-strand	267-268	2	37
α-helix	269-275	7
α-helix	281-288	8
α-helix	295-307	13
α-helix	314-322	9
β-strand	325	1	38
α-helix	332-341	10
α-helix	342-346	5
α-helix	349-351	3
α-helix	358-376	19
α-helix	381-383	3
α-helix	388-390	3
β-strand	391-394	4	36
α-helix	396-423	28
α-helix	431-434	4
α-helix	438-450	13
β-strand	468-469	2	35
α-helix	470-471	2
α-helix	475-481	7
β-strand	484-486	3	36
α-helix	503-505	3
β-strand	509	1	39
α-helix	517-519	3
β-strand	524-525	2	36
β-strand	526	1	39
β-strand	531-532	2	40
α-helix	539-547	9
β-strand	551-552	2	41
β-strand	565-569	5	41
β-strand	572-577	6	41
α-helix	580-593	14
β-strand	602-606	5	41
β-strand	611-615	5	41
β-strand	621-627	7	40
β-strand	628-629	2	42
β-strand	632-633	2	42
α-helix	637-644	8
α-helix	645-647	3
α-helix	653-658	6
β-strand	662-666	5	40
β-strand	675-676	2	40
α-helix	679-682	4
β-strand	695-696	2	40
α-helix	700-703	4
α-helix	706-709	4
α-helix	714-716	3
β-strand	717	1	43
α-helix	719-728	10
α-helix	729-731	3
β-strand	732	1	44
β-strand	734	1	45
β-strand	747-751	5	45
β-strand	755	1	46
β-strand	759-760	2	47
α-helix	762-764	3
β-strand	776-782	7	48
β-strand	794-797	4	48
α-helix	798-802	5
β-strand	808-817	10	45
β-strand	820-821	2	49
β-strand	825-826	2	49
β-strand	827-829	3	50
β-strand	837	1	50
β-strand	853	1	51
β-strand	859-861	3	45
β-strand	865-867	3	51
β-strand	869-872	4	50
β-strand	889-891	3	50
β-strand	894-895	2	51
α-helix	896-897	2
β-strand	901-911	11	45
β-strand	917-927	11	45
α-helix	928-930	3
β-strand	934-936	3	52
β-strand	943-944	2	52
β-strand	945-949	5	48
β-strand	956-957	2	53
α-helix	961-963	3
β-strand	965-967	3	48
α-helix	969-971	3
β-strand	977	1	43
α-helix	978-993	16
β-strand	997-998	2	47
α-helix	1008-1016	9
β-strand	1025-1026	2	48
β-strand	1028-1029	2	53
α-helix	1035	1
β-strand	1036	1	53
α-helix	1037	1
β-strand	1041-1048	8	48
β-strand	1049-1050	2	52
β-strand	1051	1	44
α-helix	1055-1058	4
β-strand	1060-1062	3	12
β-strand	1067	1	54
β-strand	1074	1	54
β-strand	1076	1	55
α-helix	1078-1080	3
α-helix	1082	1
β-strand	1083	1	55
β-strand	1084-1086	3	11
α-helix	1088-1096	9
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	1127-1129	3	56
β-strand	1134-1136	3	56
β-strand	1137	1	57
β-strand	1142	1	57
β-strand	1146-1150	5	1
α-helix	1153-1163	11
β-strand	1167	1	3
β-strand	1170-1172	3	2

Chain C: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	8-14	7	58
β-strand	18-24	7	58
α-helix	28-40	13
β-strand	43-55	13	59
α-helix	61-70	10
α-helix	72	1
β-strand	73	1	60
α-helix	74	1
α-helix	83-84	2
β-strand	99-106	8	59
β-strand	113-116	4	61
α-helix	117-119	3
β-strand	121-122	2	59
β-strand	129	1	60
α-helix	130-132	3
α-helix	146-148	3
β-strand	149-153	5	61
β-strand	158-169	12	59
α-helix	174-176	3
β-strand	179-186	8	58
α-helix	200-202	3
α-helix	204-206	3
α-helix	218-220	3
β-strand	228-235	8	58
α-helix	241-270	30

Chain E: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	3-24	22
β-strand	26	1	62
α-helix	30-34	5
α-helix	37-44	8
α-helix	56-58	3
β-strand	60-63	4	63
β-strand	64	1	62
β-strand	71-75	5	63
β-strand	81-82	2	64
α-helix	84-97	14
β-strand	101-106	6	63
β-strand	109-110	2	64
α-helix	112-121	10
β-strand	126-131	6	63
α-helix	132-134	3
α-helix	139-141	3
β-strand	147-150	4	65
α-helix	151-152	2
α-helix	153-163	11
α-helix	167-169	3
β-strand	172-173	2	65
α-helix	178-182	5
β-strand	190-197	8	65
β-strand	201-209	9	65

Chain F: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	56	1	66
α-helix	57-58	2
α-helix	59-74	16
α-helix	77-79	3
α-helix	89-99	11
β-strand	104-109	6	32
β-strand	115-119	5	32
α-helix	120-122	3
β-strand	124	1	66

Chain H: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-14	11	17
β-strand	25-32	8	17
β-strand	38-44	7	17
β-strand	55-61	7	17
β-strand	65	1	67
β-strand	74	1	16
β-strand	83	1	67
α-helix	84-87	4
β-strand	90-101	12	17
β-strand	111-118	8	17
β-strand	121-128	8	17
α-helix	129-132	4
β-strand	140-148	9	17

Chain I: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	68
α-helix	22	1
β-strand	23	1	68
β-strand	24-29	6	69
β-strand	34-39	6	69
β-strand	45-47	3	69
β-strand	52-57	6	30
α-helix	64-66	3
α-helix	70-74	5
β-strand	80-81	2	70
β-strand	94-97	4	70
α-helix	109-110	2
β-strand	111-114	4	70
β-strand	122-124	3	70

Chain J: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	71
β-strand	13	1	71
α-helix	18-26	9
α-helix	31-37	7
α-helix	43-51	9
β-strand	52	1	46
α-helix	56-59	4
α-helix	63-64	2

2 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 domesticus	A0A8D1DPV6
DNA-directed RNA polymerase subunit beta	B	protein	1174	Sus scrofa domesticus	A0A0B8RVL1 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB3	C	protein	275	Sus scrofa domesticus	I3LCH3 (AlphaFold model)
DNA-directed RNA polymerase II subunit E	E	protein	210	Sus scrofa domesticus	I3LSI7 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC2	F	protein	127	Sus scrofa domesticus	A0A4X1VEK9
DNA-directed RNA polymerases I, II, and III subunit RPABC3	H	protein	150	Sus scrofa domesticus	I3LCB2
DNA-directed RNA polymerase II subunit RPB9	I	protein	125	Sus scrofa domesticus	P60899
DNA-directed RNA polymerases I, II, and III subunit RPABC5	J	protein	67	Sus scrofa domesticus	A0A8W4F9W9
DNA-directed RNA polymerase II subunit RPB11-a	K	protein	117	Sus scrofa domesticus	F1RKE4
RNA polymerase II, I and III subunit K	L	protein	58	Sus scrofa domesticus	A0A4X1TRS6
Alu RNA Minimal Right Arm	R	RNA	76	Homo sapiens

Sequence of entity 1 (A), FASTA

>8QEQ_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

>8QEQ_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

>8QEQ_3 DNA-directed RNA polymerase II subunit RPB3 (chains C)
MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH
DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL
ISNSPRVIPVTSRNRDNDPSDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR
PETIVLSALSGLKKKLSDLQTQLSHEIQSDVLTIN

Sequence of entity 4 (E), FASTA

>8QEQ_4 DNA-directed RNA polymerase II subunit E (chains E)
MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTV
LVAHNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVD
MAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVA
RYFGIKRGQVVKIIRPSETAGRYITYRLVQ

Sequence of entity 5 (F), FASTA

>8QEQ_5 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKY
ERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGV
DELIISD

Sequence of entity 6 (H), FASTA

>8QEQ_6 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVI
ASTLYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGG
LLMRLQGDANNLHGFEVDSRVYLLMKKLAF

Sequence of entity 7 (I), FASTA

>8QEQ_7 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MEPDGTYEPGFVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITH
EVDELTQIIADVSQDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCG
HRWTE

Sequence of entity 8 (J), FASTA

>8QEQ_8 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL
NYAPLEK

Sequence of entity 9 (K), FASTA

>8QEQ_9 DNA-directed RNA polymerase II subunit RPB11-a (chains K)
MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG
YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVAIKDKQEGIE

Sequence of entity 10 (L), FASTA

>8QEQ_10 RNA polymerase II, I and III subunit K (chains L)
MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR

Sequence of entity 11 (R), FASTA

>8QEQ_11 Alu RNA Minimal Right Arm (chains R)
GAGGCAGGAGAAUGGCGUGAACCCGGGAGGUGGACGAGAUCGCUCCAGCCUGGGUGACAG
AGCGAGACUCUGUCUC

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
ZN	Zinc ion	Zn	7

Primary citation

Mechanism of mammalian transcriptional repression by noncoding RNA. Tluckova, K., Kaczmarek, B., Salmazo, A. et al. Nat Struct Mol Biol (2025) 32:607-612. DOI 10.1038/s41594-024-01448-7 · 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

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