9ZP4: DNA-directed RNA polymerase subunit alpha

E. coli RNA polymerase elongation complex containing the unnatural dZ:PTP base pair in a trigger-loop-closed conformation. Determined by electron microscopy at 2.42 Å resolution. Released 2 Sept 2026.

Method: Electron microscopy
Resolution: 2.42 Å
Organism: Escherichia coli
Chains: 8
Atoms: 26,654
Mol. weight: 382.15 kDa
Ligands: MG, ZN, A1C5A
Released: 2 Sept 2026

Explore 9ZP4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9ZP4 contains 158 α-helices and 219 β-strands across 5 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, 18 β-strands

Element	Residues	Length	Sheet
β-strand	13-15	3	1
β-strand	18	1	1
β-strand	23-31	9	1
α-helix	35-49	15
β-strand	53-61	9	2
β-strand	74	1	3
α-helix	78-87	10
β-strand	90-91	2	4
β-strand	97-101	5	2
β-strand	104-105	2	5
β-strand	108-111	4	3
α-helix	112-114	3
β-strand	122-123	2	4
β-strand	129-133	5	3
β-strand	139-140	2	5
β-strand	142-149	8	2
β-strand	152-153	2	6
α-helix	166-167	2
β-strand	170-172	3	2
β-strand	175-176	2	6
β-strand	180-192	13	1
β-strand	195-207	13	1
α-helix	213-229	17

Chain G: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	7
β-strand	23-31	9	7
α-helix	35-49	15
β-strand	52-53	2	8
β-strand	56-61	6	9
β-strand	74	1	10
α-helix	78-86	9
β-strand	90-92	3	11
β-strand	97-105	9	9
β-strand	108-111	4	10
α-helix	112-114	3
β-strand	115	1	9
α-helix	116-117	2
β-strand	121-123	3	11
β-strand	129-133	5	10
β-strand	139-147	9	9
β-strand	149-150	2	8
β-strand	151-153	3	12
α-helix	155-161	7
β-strand	171-172	2	9
β-strand	175-177	3	12
β-strand	180-189	10	7
β-strand	192	1	13
β-strand	195	1	13
β-strand	199-207	9	7
α-helix	213-232	20

Chain I: 63 helices, 94 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
α-helix	11-12	2
β-strand	13-14	2	14
α-helix	23-26	4
α-helix	29-39	11
α-helix	48-54	7
α-helix	57	1
β-strand	59-60	2	15
β-strand	66-75	10	15
α-helix	82-88	7
β-strand	93-105	13	15
β-strand	114-128	15	15
β-strand	136-138	3	16
β-strand	141-145	5	16
α-helix	146	1
β-strand	147-151	5	17
α-helix	152	1
β-strand	154-159	6	18
β-strand	172-177	6	18
β-strand	180	1	19
β-strand	184-188	5	18
β-strand	194-198	5	18
β-strand	204-205	2	18
α-helix	207-212	6
α-helix	217-224	8
β-strand	227-232	6	20
β-strand	237-240	4	20
α-helix	243-246	4
β-strand	255-257	3	21
β-strand	260-263	4	21
α-helix	271-280	10
β-strand	284-286	3	20
α-helix	289-291	3
β-strand	296-297	2	20
β-strand	301-302	2	22
β-strand	309-311	3	22
β-strand	315-316	2	20
α-helix	319-328	10
β-strand	332-336	5	20
α-helix	346-350	5
α-helix	351-353	3
α-helix	359-370	12
α-helix	378-389	12
β-strand	396	1	19
α-helix	398-408	11
α-helix	422-437	16
β-strand	451-454	4	17
α-helix	456-478	23
α-helix	489-491	3
α-helix	496-508	13
β-strand	512-514	3	16
α-helix	515-516	2
α-helix	520-527	8
β-strand	529-531	3	17
α-helix	550-551	2
α-helix	552-554	3
β-strand	558	1	23
β-strand	572-574	3	17
β-strand	575	1	23
β-strand	580-581	2	24
β-strand	587-595	9	24
β-strand	598-607	10	24
α-helix	608-611	4
β-strand	616-617	2	24
β-strand	623	1	25
β-strand	628	1	24
β-strand	629	1	25
β-strand	633-638	6	24
β-strand	641-646	6	24
β-strand	652-654	3	24
α-helix	665-667	3
α-helix	671-673	3
β-strand	674	1	26
α-helix	676-686	11
β-strand	689	1	27
α-helix	690-691	2
β-strand	700-701	2	14
α-helix	705-712	8
β-strand	716-717	2	28
β-strand	722-727	6	29
β-strand	731-736	6	29
α-helix	738-740	3
β-strand	748-752	5	29
α-helix	753-754	2
β-strand	757-758	2	30
β-strand	763	1	31
β-strand	764-765	2	30
β-strand	768-769	2	28
β-strand	776-777	2	29
β-strand	782-785	4	28
β-strand	789-790	2	32
β-strand	793-794	2	32
β-strand	798-804	7	33
β-strand	815-819	5	33
α-helix	820-824	5
β-strand	830-841	12	31
β-strand	842-843	2	34
β-strand	846-847	2	34
β-strand	849-850	2	35
α-helix	859-862	4
β-strand	865	1	36
β-strand	870	1	37
β-strand	871	1	36
α-helix	872	1
β-strand	876-877	2	31
β-strand	882-884	3	37
β-strand	886-889	4	35
β-strand	913-915	3	35
β-strand	918-919	2	37
α-helix	920-921	2
β-strand	926-935	10	31
β-strand	936	1	38
α-helix	943-981	39
α-helix	986-991	6
α-helix	994-997	4
α-helix	1005-1037	33
β-strand	1040	1	38
β-strand	1046-1058	13	31
β-strand	1065-1067	3	33
β-strand	1073-1080	8	33
α-helix	1082-1084	3
β-strand	1087	1	39
α-helix	1092	1
β-strand	1093	1	39
α-helix	1094	1
β-strand	1096-1098	3	33
α-helix	1102-1106	5
β-strand	1108	1	26
α-helix	1110-1133	24
α-helix	1138-1150	13
α-helix	1161-1163	3
α-helix	1166-1175	10
β-strand	1182-1183	2	14
α-helix	1192-1201	10
β-strand	1209-1210	2	40
β-strand	1213	1	39
α-helix	1219	1
β-strand	1220	1	39
α-helix	1221	1
β-strand	1225-1226	2	40
β-strand	1227-1234	8	33
β-strand	1235	1	27
α-helix	1239-1241	3
β-strand	1244-1246	3	41
β-strand	1251	1	42
α-helix	1257	1
β-strand	1258	1	42
α-helix	1259	1
β-strand	1260	1	43
α-helix	1262-1264	3
β-strand	1267	1	43
β-strand	1268-1270	3	44
α-helix	1272-1281	10
α-helix	1284-1291	8
α-helix	1298-1310	13
α-helix	1321-1331	11
β-strand	1335-1340	6	45

Chain J: 77 helices, 87 β-strands

Element	Residues	Length	Sheet
β-strand	19-24	6	45
α-helix	27-33	7
β-strand	34-37	4	46
β-strand	44	1	47
β-strand	51	1	47
α-helix	52	1
α-helix	59-62	4
β-strand	66	1	48
β-strand	69	1	48
β-strand	76	1	48
β-strand	84	1	49
β-strand	91	1	49
α-helix	95-99	5
β-strand	102-112	11	46
α-helix	115-118	4
α-helix	122	1
α-helix	123-128	6
α-helix	132-139	8
β-strand	144-148	5	50
β-strand	159-160	2	50
α-helix	162-171	10
β-strand	177-179	3	50
α-helix	182-190	9
α-helix	194-207	14
α-helix	211-230	20
α-helix	234-237	4
β-strand	238-244	7	46
α-helix	247-249	3
β-strand	253-254	2	51
β-strand	260-261	2	51
α-helix	264-284	21
α-helix	289-307	19
α-helix	315-316	2
β-strand	317	1	52
β-strand	323	1	52
α-helix	324-325	2
α-helix	328-330	3
α-helix	337	1
α-helix	338-342	5
β-strand	345-347	3	44
β-strand	350-354	5	41
β-strand	355-357	3	53
β-strand	365-369	5	53
α-helix	370-376	7
α-helix	378-387	10
α-helix	394-403	10
α-helix	406-416	11
β-strand	421-424	4	41
α-helix	431-433	3
β-strand	434-437	4	41
β-strand	438-442	5	53
β-strand	447-449	3	53
α-helix	451-453	3
α-helix	454-457	4
β-strand	465-469	5	41
α-helix	474-479	6
α-helix	480-484	5
β-strand	485	1	41
α-helix	486-488	3
β-strand	491	1	54
β-strand	498	1	54
α-helix	505-513	9
β-strand	526-527	2	55
α-helix	530-539	10
β-strand	547-556	10	55
β-strand	564-573	10	55
α-helix	574-579	6
α-helix	580-582	3
α-helix	584	1
α-helix	589-591	3
α-helix	598-611	14
α-helix	614-635	22
α-helix	641-643	3
α-helix	645-647	3
α-helix	650-669	20
α-helix	675-701	27
β-strand	703-707	5	56
β-strand	713-717	5	56
α-helix	721-728	8
α-helix	734-741	8
β-strand	745	1	57
β-strand	747	1	58
β-strand	748	1	59
α-helix	753	1
β-strand	754	1	59
α-helix	755	1
α-helix	758	1
β-strand	759	1	57
α-helix	769-788	20
α-helix	790-803	14
β-strand	809-811	3	60
β-strand	820-822	3	61
β-strand	825-826	2	62
β-strand	831-833	3	62
α-helix	835-839	5
β-strand	843	1	63
β-strand	844	1	61
α-helix	847	1
β-strand	848-849	2	64
α-helix	850	1
β-strand	856-858	3	64
β-strand	863	1	63
α-helix	866-874	9
β-strand	880-882	3	61
α-helix	885-887	3
β-strand	894-895	2	60
α-helix	896-899	4
β-strand	901-902	2	65
β-strand	907-908	2	65
α-helix	909-910	2
α-helix	915-931	17
α-helix	934-937	4
β-strand	940	1	58
α-helix	945-947	3
β-strand	949-951	3	66
β-strand	956-961	6	67
β-strand	965-967	3	66
β-strand	973-975	3	66
β-strand	980-985	6	67
β-strand	991-997	7	67
β-strand	1002-1003	2	66
β-strand	1010-1011	2	67
β-strand	1016-1019	4	66
β-strand	1024-1028	5	68
β-strand	1033-1038	6	69
β-strand	1042	1	70
β-strand	1046	1	70
β-strand	1048	1	68
β-strand	1059-1060	2	68
β-strand	1077-1081	5	69
α-helix	1086	1
β-strand	1087	1	69
α-helix	1088	1
β-strand	1089	1	71
α-helix	1090	1
β-strand	1096	1	71
β-strand	1098-1100	3	69
β-strand	1106-1107	2	68
β-strand	1114-1115	2	69
β-strand	1120-1125	6	68
α-helix	1134-1145	12
α-helix	1148-1150	3
β-strand	1155-1156	2	72
β-strand	1161-1165	5	73
α-helix	1167-1169	3
β-strand	1172-1178	7	73
β-strand	1186-1191	6	73
β-strand	1203-1204	2	73
β-strand	1209-1211	3	72
α-helix	1214-1216	3
α-helix	1217-1224	8
α-helix	1226-1243	18
α-helix	1250-1260	11
β-strand	1263-1268	6	74
β-strand	1279-1281	3	74
α-helix	1282-1294	13
β-strand	1301-1304	4	74
α-helix	1309-1313	5
α-helix	1319-1325	7
α-helix	1328-1338	11
β-strand	1341-1342	2	45
α-helix	1347-1353	7
α-helix	1360-1362	3
α-helix	1363-1372	10

Chain K: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	7-13	7
α-helix	20-22	3
α-helix	23-27	5
α-helix	28-31	4
α-helix	35-37	3
α-helix	46-56	11
α-helix	61-72	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA-directed RNA polymerase subunit alpha	A, G	protein	231	Escherichia coli	P0A7Z4 (AlphaFold model)
DNA-directed RNA polymerase subunit beta	I	protein	1342	Escherichia coli	P0A8V2 (AlphaFold model)
DNA-directed RNA polymerase subunit beta'	J	protein	1430	Escherichia coli	P0A8T7 (AlphaFold model)
DNA-directed RNA polymerase subunit omega	K	protein	74	Escherichia coli	P0A800 (AlphaFold model)
Non-template strand DNA	N	DNA	11	Escherichia coli
RNA	R	RNA	9	Escherichia coli
Template strand DNA	T	DNA	22	Escherichia coli

Sequence of entity 1 (A, G), FASTA

>9ZP4_1 DNA-directed RNA polymerase subunit alpha (chains A, G)
SVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDG
VLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEI
VKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERI
AYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDL

Sequence of entity 2 (I), FASTA

>9ZP4_2 DNA-directed RNA polymerase subunit beta (chains I)
MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQ
SYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQ
EVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYR
GSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQME
LVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKD
YIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRL
SALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGIL
SKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLS
LGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTR
ERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVT
DEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQV
VSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKR
GGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERG
DVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVS
RDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEK
LLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDL
SEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDE
LKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKIN
PIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAK
LREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLK
LGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLG
GKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMP
ESFNVLLKEIRSLGINIELEDE

Sequence of entity 3 (J), FASTA

>9ZP4_3 DNA-directed RNA polymerase subunit beta' (chains J)
MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCAR
IFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSL
PSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDEFDAKM
GAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILT
VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQ
EAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPY
LRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHP
VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA
RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSG
LASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKA
ISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAE
VAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFN
SIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGAR
KGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVL
GRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYG
RDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKL
SNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANW
DPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKI
VDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDITGGLPR
VADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFE
GERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQM
LRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFI
SAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAGEAPA
APQVTAEDASASLAELLNAGLGGSDNELELEVLFQGPSSGHHHHHHHHHH

Sequence of entity 4 (K), FASTA

>9ZP4_4 DNA-directed RNA polymerase subunit omega (chains K)
MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLIN
NQILDVRERQEQQE

Sequence of entity 5 (N), FASTA

>9ZP4_5 Non-template strand DNA (chains N)
TCAGCGAGAGA

Sequence of entity 6 (R), FASTA

>9ZP4_6 RNA (chains R)
AUCGAGAGG

Sequence of entity 7 (T), FASTA

>9ZP4_7 Template strand DNA (chains T)
TCTCTCGCTGAXCCTCTCGATG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	2
A1C5A	(5S)-2-amino-8-{5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosp…	C10 H16 N5 O14 P3	1

Primary citation

Structural basis of transcription of the hachimoji eight-letter alphabet by E. coli RNA polymerase. Li, Q., Kim, H.J., Liu, Y. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-76668-0 · PubMed

Other PDB entries of the same protein (UniProt P0A7Z4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3K4G 2.05 Å, Crystal structure of E. coli RNA polymerase alpha subunit C-terminal domain
8FVW 2.1 Å, CryoEM structure of E.coli transcription elongation complex bound to ppGpp
8FVR 2.42 Å, CryoEM structure of E.coli transcription elongation complex
8HKC 2.49 Å, Cryo-EM structure of E. coli RNAP sigma32 complex
1BDF 2.5 Å, Structure of escherichia coli RNA polymerase alpha subunit N-terminal domain
6XL5 2.5 Å, Cryo-EM structure of EcmrR-RNAP-promoter open complex (EcmrR-RPo)
6XL9 2.5 Å, Cryo-EM structure of EcmrR-RNAP-promoter initial transcribing complex with 3-nt RNA…
12EC 2.6 Å, Half-translocated RNA polymerase elemental paused elongation complex, swiveled (ePEC…
8F1J 2.6 Å, SigN RNA polymerase early-melted intermediate bound to mismatch DNA fragment dhsU36mm2…
8PIB 2.6 Å, autoinhibited RfaH bound to E. coli transcription complex paused at ops site (encounter…
9MSF 2.6 Å, de novo SigN RNA polymerase transcription initiation intermediate with post-catalytic…
9YMV 2.6 Å, De novo initial transcribing RNA polymerase with pretranslocated 3-mer RNA / product…

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