9EHZ: DNA-directed RNA polymerase II subunit RPB4

Cryo-EM structure of Human RNA polymerase II Elongation Complex in an Intermediate Translocation State. Determined by electron microscopy at 2.6 Å resolution. Released 5 Mar 2025.

Method: Electron microscopy
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 15
Atoms: 32,125
Mol. weight: 546.22 kDa
Ligands: MG, ZN
Released: 5 Mar 2025

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

Secondary structure: helices and β-sheets

9EHZ contains 180 α-helices and 226 β-strands across 12 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: 77 helices, 70 β-strands

Element	Residues	Length	Sheet
α-helix	14	1
β-strand	15-16	2	21
β-strand	20-22	3	22
β-strand	25	1	23
α-helix	28-34	7
β-strand	47	1	24
β-strand	52	1	24
α-helix	53	1
β-strand	86-95	10	25
α-helix	100-108	9
β-strand	110-111	2	26
β-strand	114-117	4	26
α-helix	124-132	9
α-helix	137-148	12
β-strand	153	1	27
β-strand	187	1	27
β-strand	190-194	5	28
β-strand	197-201	5	28
β-strand	213-216	4	28
α-helix	218-226	9
α-helix	230-235	6
α-helix	245-248	4
β-strand	249-255	7	25
α-helix	262-263	2
β-strand	264-266	3	29
β-strand	270-272	3	29
α-helix	275-296	22
α-helix	302-318	17
α-helix	326-328	3
β-strand	329	1	30
β-strand	335	1	30
α-helix	339-343	5
α-helix	349	1
α-helix	350-354	5
β-strand	357-358	2	31
β-strand	362-369	8	32
β-strand	377-381	5	32
α-helix	382-387	6
β-strand	389-393	5	33
α-helix	399-408	10
β-strand	416-420	5	33
β-strand	426-428	3	33
α-helix	435-438	4
β-strand	445-449	5	33
α-helix	450	1
β-strand	455-459	5	32
α-helix	466-468	3
β-strand	469-477	9	32
β-strand	482-484	3	32
α-helix	486-488	3
α-helix	489-492	4
β-strand	500-504	5	32
α-helix	509-518	10
β-strand	520	1	32
α-helix	521-524	4
β-strand	526-527	2	34
β-strand	532-533	2	34
α-helix	539-548	10
β-strand	554-555	2	35
α-helix	557-564	8
α-helix	573-574	2
β-strand	575	1	11
α-helix	576-577	2
β-strand	579-581	3	10
β-strand	585	1	10
β-strand	586-587	2	35
α-helix	588-593	6
β-strand	602-604	3	36
β-strand	628-631	4	36
β-strand	634-638	5	36
α-helix	642-645	4
α-helix	652-659	8
α-helix	662-683	22
β-strand	686	1	37
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	38
β-strand	792-793	2	39
β-strand	796-797	2	39
α-helix	798-799	2
β-strand	802	1	40
β-strand	805	1	40
β-strand	822-823	2	38
α-helix	833-867	35
β-strand	872-873	2	41
β-strand	879-880	2	41
β-strand	886-888	3	41
α-helix	891-893	3
β-strand	896	1	42
β-strand	902-905	4	43
α-helix	913-920	8
α-helix	929-933	5
β-strand	934	1	44
α-helix	936-944	9
α-helix	946-969	24
α-helix	971-973	3
β-strand	976-979	4	43
α-helix	983-993	11
β-strand	1002	1	44
α-helix	1006-1019	14
α-helix	1028-1037	10
α-helix	1039-1048	10
α-helix	1051-1053	3
α-helix	1054-1058	5
α-helix	1062-1079	18
β-strand	1080	1	42
α-helix	1081-1082	2
α-helix	1087-1099	13
α-helix	1120-1129	10
β-strand	1138-1142	5	45
α-helix	1146-1149	4
α-helix	1151-1161	11
β-strand	1164	1	46
α-helix	1167-1169	3
β-strand	1170-1177	8	15
α-helix	1187-1189	3
α-helix	1190-1193	4
β-strand	1210-1216	7	15
α-helix	1217	1
α-helix	1218-1222	5
α-helix	1228-1239	12
β-strand	1245-1247	3	15
β-strand	1255-1259	5	15
α-helix	1281-1295	15
β-strand	1299	1	46
β-strand	1306-1310	5	45
α-helix	1315-1317	3
β-strand	1319-1322	4	47
β-strand	1328-1331	4	47
β-strand	1335-1339	5	45
α-helix	1343-1348	6
β-strand	1358-1359	2	45
α-helix	1362-1368	7
α-helix	1371-1387	17
α-helix	1395-1406	12
α-helix	1416-1419	4
α-helix	1426-1429	4
α-helix	1436-1445	10
β-strand	1448-1449	2	22
α-helix	1454-1459	6
β-strand	1471-1475	5	7
α-helix	1477-1480	4

Chain B: 52 helices, 82 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	48
β-strand	83-93	11	48
β-strand	97-100	4	49
β-strand	104-107	4	49
α-helix	108-109	2
α-helix	110-116	7
β-strand	121-133	13	48
β-strand	141-153	13	48
α-helix	154-155	2
α-helix	168-173	6
β-strand	185-187	3	50
β-strand	190-193	4	50
α-helix	194-195	2
β-strand	196-200	5	51
α-helix	201	1
β-strand	205-208	4	52
β-strand	215-225	11	52
β-strand	229-240	12	52
β-strand	256-259	4	52
β-strand	263	1	53
β-strand	267-268	2	52
α-helix	269-274	6
α-helix	281-288	8
α-helix	295-307	13
α-helix	314-323	10
β-strand	325	1	53
α-helix	332-341	10
α-helix	342-346	5
α-helix	355-357	3
α-helix	358-377	20
α-helix	381-383	3
α-helix	388-390	3
β-strand	391-394	4	51
α-helix	396-423	28
α-helix	437-450	14
β-strand	453	1	54
β-strand	463	1	54
α-helix	464	1
β-strand	468-469	2	50
α-helix	470	1
α-helix	475-482	8
β-strand	484-486	3	51
α-helix	503-505	3
β-strand	509	1	55
β-strand	524-525	2	51
β-strand	526	1	55
β-strand	531-532	2	56
α-helix	539-547	9
β-strand	551-552	2	57
α-helix	558-560	3
β-strand	565-569	5	57
β-strand	572-577	6	57
α-helix	580-593	14
β-strand	602-606	5	57
β-strand	611-615	5	57
β-strand	621-627	7	56
β-strand	628-629	2	58
β-strand	632-633	2	58
α-helix	637-644	8
α-helix	653-658	6
β-strand	662-666	5	56
α-helix	667-670	4
β-strand	675-676	2	56
α-helix	679-682	4
β-strand	695-696	2	56
α-helix	700-703	4
α-helix	707-710	4
α-helix	714-716	3
β-strand	717	1	59
α-helix	719-729	11
β-strand	732	1	60
β-strand	735	1	19
β-strand	748-751	4	19
β-strand	755	1	17
β-strand	759-760	2	61
β-strand	776-782	7	62
β-strand	783	1	37
β-strand	794-797	4	62
α-helix	798-802	5
β-strand	808-817	10	19
β-strand	827-829	3	63
β-strand	837	1	63
β-strand	848	1	64
β-strand	853	1	65
β-strand	854	1	64
α-helix	855	1
β-strand	859-860	2	19
β-strand	865-867	3	65
β-strand	869-872	4	63
β-strand	889-891	3	63
β-strand	894-895	2	65
α-helix	896-897	2
β-strand	902-911	10	19
β-strand	917-927	11	19
β-strand	934-937	4	62
β-strand	942-949	8	62
β-strand	956	1	66
β-strand	965-967	3	62
α-helix	969-971	3
β-strand	977	1	59
α-helix	978-993	16
β-strand	997-998	2	61
α-helix	1008-1016	9
β-strand	1025-1026	2	62
β-strand	1029	1	66
α-helix	1035	1
β-strand	1036	1	66
α-helix	1037	1
β-strand	1041-1050	10	62
β-strand	1051	1	60
β-strand	1060-1062	3	32
β-strand	1067	1	67
β-strand	1074	1	67
α-helix	1075	1
α-helix	1082-1084	3
β-strand	1085-1086	2	31
α-helix	1088-1097	10
α-helix	1100-1104	5
α-helix	1105-1110	6
β-strand	1113-1119	7	21
β-strand	1125	1	21
β-strand	1127-1129	3	68
β-strand	1134-1136	3	68
β-strand	1137	1	69
β-strand	1142	1	69
β-strand	1146-1152	7	21
α-helix	1153-1164	12
β-strand	1167	1	23
β-strand	1170-1172	3	22

Chain C: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	8-14	7	70
β-strand	18-24	7	70
α-helix	28-39	12
β-strand	44-55	12	20
α-helix	61-69	9
α-helix	78-81	4
β-strand	99-106	8	20
β-strand	113-116	4	71
α-helix	117-119	3
β-strand	121-122	2	20
β-strand	149-153	5	71
β-strand	158-168	11	20
α-helix	174-176	3
β-strand	179	1	72
β-strand	183-185	3	70
α-helix	200-202	3
α-helix	204-206	3
α-helix	218-220	3
β-strand	229-234	6	70
β-strand	235	1	72
α-helix	241-270	30

Chain D: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	1
β-strand	21	1	1
α-helix	29-31	3
α-helix	34-49	16
α-helix	55-58	4
α-helix	59-70	12
α-helix	77-88	12
α-helix	94-103	10
α-helix	108-114	7
α-helix	116-118	3
α-helix	124-137	14

Chain E: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	4-23	20
β-strand	26	1	2
α-helix	30-33	4
α-helix	37-43	7
β-strand	60-61	2	3
β-strand	64	1	2
β-strand	73-75	3	3
β-strand	81-82	2	4
α-helix	84-97	14
β-strand	101-106	6	3
β-strand	109-110	2	4
α-helix	112-120	9
β-strand	126-131	6	3
α-helix	134-136	3
α-helix	139-141	3
β-strand	147-150	4	5
α-helix	151-152	2
α-helix	153-162	10
α-helix	167-169	3
β-strand	172-173	2	5
α-helix	178-183	6
α-helix	185-186	2
β-strand	190-196	7	5
β-strand	202-209	8	5

Chain F: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	56	1	6
α-helix	57-58	2
α-helix	59-74	16
α-helix	77-79	3
α-helix	89-98	10
β-strand	104-109	6	7
β-strand	115-119	5	7
β-strand	124	1	6
α-helix	125	1

Chain G: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2-13	12	7
α-helix	15-17	3
α-helix	22-34	13
β-strand	38-39	2	7
β-strand	43-54	12	7
β-strand	57-59	3	7
α-helix	65	1
β-strand	66-77	12	7
β-strand	84-92	9	8
β-strand	96-101	6	8
β-strand	104-109	6	8
β-strand	117-120	4	9
β-strand	127-130	4	9
β-strand	136-137	2	9
β-strand	142-153	12	8
β-strand	156-162	7	8
β-strand	170	1	8

Chain H: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-14	11	10
β-strand	25-32	8	10
β-strand	38-44	7	10
β-strand	55-61	7	10
β-strand	74	1	11
β-strand	90-101	12	10
β-strand	104	1	12
β-strand	107	1	12
α-helix	108-109	2
β-strand	111-118	8	10
β-strand	121-128	8	10
β-strand	139-147	9	10

4 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 RPB4	D	protein	142	Homo sapiens	O15514 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC1	E	protein	210	Homo sapiens	P19388 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC2	F	protein	127	Homo sapiens	P61218 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB7	G	protein	172	Homo sapiens	P62487 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC3	H	protein	150	Homo sapiens	P52434
DNA-directed RNA polymerase II subunit RPB9	I	protein	125	Homo sapiens	P36954
DNA-directed RNA polymerases I, II, and III subunit RPABC5	J	protein	67	Homo sapiens	P62875
DNA-directed RNA polymerase II subunit RPB11-a	K	protein	117	Homo sapiens	P52435
DNA-directed RNA polymerases I, II, and III subunit RPABC4	L	protein	58	Homo sapiens	P53803
Non-template DNA, nucleic acid scaffold	N	DNA	43	Homo sapiens
RNA, nucleic acid scaffold	P	RNA	20	Homo sapiens
Template DNA, nucleic acid scaffold	T	DNA	28	Homo sapiens

3 more molecules are not listed.

Sequence of entity 1 (D), FASTA

>9EHZ_1 DNA-directed RNA polymerase II subunit RPB4 (chains D)
MAAGGSDPRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEV
FMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEG
RFEDEELQQILDDIQTKRSFQY

Sequence of entity 2 (E), FASTA

>9EHZ_2 DNA-directed RNA polymerases I, II, and III subunit RPABC1 (chains E)
MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTV
LVAHNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVD
MAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVA
RYFGIKRGQVVKIIRPSETAGRYITYRLVQ

Sequence of entity 3 (F), FASTA

>9EHZ_3 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKY
ERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGV
DELIITD

Sequence of entity 4 (G), FASTA

>9EHZ_4 DNA-directed RNA polymerase II subunit RPB7 (chains G)
MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQ
PGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFD
PNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAIGSLMDDYLGLVS

Sequence of entity 5 (H), FASTA

>9EHZ_5 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVI
ASTLYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGG
LLMRLQGDANNLHGFEVDSRVYLLMKKLAF

Sequence of entity 6 (I), FASTA

>9EHZ_6 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MEPDGTYEPGFVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITH
EVDELTQIIADVSQDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCG
HRWTE

Sequence of entity 7 (J), FASTA

>9EHZ_7 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL
NYAPLEK

Sequence of entity 8 (K), FASTA

>9EHZ_8 DNA-directed RNA polymerase II subunit RPB11-a (chains K)
MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG
YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVAIKDKQEGIE

Sequence of entity 9 (L), FASTA

>9EHZ_9 DNA-directed RNA polymerases I, II, and III subunit RPABC4 (chains L)
MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR

Sequence of entity 10 (N), FASTA

>9EHZ_10 Non-template DNA, nucleic acid scaffold (chains N)
TAGTAAACTAGTATTGAAAGTACTTGAGCTTAGACAGCATGTC

Sequence of entity 11 (P), FASTA

>9EHZ_11 RNA, nucleic acid scaffold (chains P)
UAUAUGCAUAAAGACCAGGC

Sequence of entity 12 (T), FASTA

>9EHZ_12 Template DNA, nucleic acid scaffold (chains T)
CTCAAGTACTTACGCCTGGTCATTACTA

Ligands and cofactors

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

Primary citation

Structural insights into transcriptional regulation by the helicase RECQL5. Florez Ariza, A.J., Lue, N.Z., Grob, P. et al. Nat Struct Mol Biol (2025) 32:1721-1730. DOI 10.1038/s41594-025-01611-8 · PubMed

Other PDB entries of the same protein (UniProt O15514 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2C35 2.7 Å, Subunits Rpb4 and Rpb7 of human RNA polymerase II
8XSO 2.7 Å, RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei
9T5H 2.7 Å, RNA polymerase II bound to Gdown1 and RPAP2
28JC 2.94 Å, RNA polymerase II bound to RPAP2 and Gdown1
8XRM 3.13 Å, RNA polymerase II elongation complex with DSIF, SPT6, and ELOF1 transcribing genomic DNA…
9EI1 3.2 Å, Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5…
9EI3 3.2 Å, Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5…
8XRJ 3.6 Å, RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei
9EI4 3.7 Å, Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5…
5IYB 3.9 Å, Human core-PIC in the open state
5IYC 3.9 Å, Human core-PIC in the initial transcribing state
5IYD 3.9 Å, Human core-PIC in the initial transcribing state (no IIS)

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