12EC: DNA-directed RNA polymerase subunit alpha

Half-translocated RNA polymerase elemental paused elongation complex, swiveled (ePEC swiveled). Determined by electron microscopy at 2.6 Å resolution. Released 1 Jul 2026.

Method: Electron microscopy
Resolution: 2.6 Å
Organism: Escherichia coli
Chains: 8
Atoms: 27,404
Mol. weight: 441.21 kDa
Ligands: 1N7, MG, ZN
Released: 1 Jul 2026

Explore 12EC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

12EC contains 162 α-helices and 208 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 G: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
β-strand	12-20	9	1
β-strand	23-31	9	1
α-helix	35-49	15
β-strand	52-61	10	2
β-strand	74	1	3
α-helix	78-85	8
β-strand	90-92	3	4
β-strand	97-105	9	2
β-strand	108-111	4	3
α-helix	112-114	3
β-strand	115	1	2
α-helix	116-117	2
β-strand	121-123	3	4
β-strand	129-133	5	3
β-strand	139-150	12	2
β-strand	152-153	2	5
β-strand	170-172	3	2
β-strand	175-176	2	5
β-strand	180-189	10	1
β-strand	199-207	9	1
α-helix	213-227	15
α-helix	229-232	4

Chain H: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	13-20	8	6
β-strand	23-31	9	6
α-helix	35-49	15
β-strand	52-61	10	7
β-strand	74	1	8
α-helix	78-86	9
β-strand	90-92	3	9
β-strand	97-105	9	7
β-strand	108-111	4	8
α-helix	112-114	3
β-strand	115	1	7
α-helix	116-117	2
β-strand	121-123	3	9
β-strand	129-133	5	8
β-strand	139-150	12	7
β-strand	152-153	2	10
α-helix	155-157	3
β-strand	170-172	3	7
β-strand	175-176	2	10
β-strand	180-192	13	6
β-strand	195-207	13	6
α-helix	213-227	15

Chain I: 71 helices, 94 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
α-helix	11-12	2
β-strand	13-14	2	11
α-helix	19-20	2
α-helix	23-26	4
α-helix	29-39	11
α-helix	49-54	6
β-strand	59-60	2	12
β-strand	66-75	10	12
α-helix	76-78	3
α-helix	82-88	7
β-strand	93-105	13	12
β-strand	114-128	15	12
β-strand	130	1	13
β-strand	136-138	3	13
β-strand	141-145	5	13
β-strand	147-151	5	14
α-helix	152	1
β-strand	154-159	6	15
β-strand	172-177	6	15
β-strand	180	1	16
β-strand	184-188	5	15
β-strand	194-198	5	15
β-strand	204-205	2	15
α-helix	206-212	7
α-helix	217-224	8
β-strand	227-232	6	17
β-strand	237-240	4	17
α-helix	243-246	4
β-strand	250	1	18
β-strand	255-257	3	19
β-strand	260-263	4	19
α-helix	267	1
β-strand	268	1	18
α-helix	269	1
α-helix	271-280	10
β-strand	284-286	3	17
α-helix	289-294	6
β-strand	296	1	20
β-strand	297	1	17
β-strand	301-302	2	21
β-strand	309-311	3	21
β-strand	316	1	20
α-helix	319-328	10
β-strand	332-336	5	17
α-helix	346-353	8
α-helix	359-370	12
α-helix	378-389	12
β-strand	396	1	16
α-helix	398-408	11
α-helix	422-436	15
α-helix	448-450	3
β-strand	451-454	4	14
α-helix	456-481	26
α-helix	484-486	3
α-helix	489-492	4
α-helix	496-508	13
β-strand	512-514	3	13
α-helix	520-527	8
β-strand	529-531	3	14
α-helix	546-548	3
α-helix	552-554	3
β-strand	558	1	22
β-strand	572-574	3	14
β-strand	575	1	22
β-strand	576	1	23
β-strand	580-581	2	24
β-strand	587-594	8	24
β-strand	598	1	25
β-strand	599-607	9	24
α-helix	608-611	4
β-strand	616-617	2	24
β-strand	623	1	26
β-strand	628	1	25
β-strand	629	1	26
β-strand	633-638	6	24
β-strand	641-646	6	24
α-helix	647-649	3
β-strand	652-654	3	24
β-strand	662	1	23
α-helix	665-667	3
α-helix	671-673	3
α-helix	676-685	10
β-strand	689	1	27
α-helix	690-691	2
β-strand	700-701	2	11
α-helix	705-712	8
β-strand	716-717	2	28
β-strand	722-728	7	29
β-strand	731-736	6	29
α-helix	738-740	3
α-helix	741-742	2
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	1	32
β-strand	794	1	32
β-strand	798-804	7	33
α-helix	812-814	3
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
α-helix	940-941	2
α-helix	943-981	39
α-helix	986-989	4
α-helix	994-997	4
α-helix	1007-1037	31
α-helix	1038-1040	3
α-helix	1042-1043	2
β-strand	1046-1058	13	31
α-helix	1059-1060	2
β-strand	1065-1067	3	33
β-strand	1073-1080	8	33
α-helix	1082-1084	3
β-strand	1087	1	38
α-helix	1092	1
β-strand	1093	1	38
α-helix	1094	1
β-strand	1096-1098	3	33
α-helix	1100-1102	3
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	11
α-helix	1192-1201	10
β-strand	1209-1210	2	33
β-strand	1213	1	38
β-strand	1220	1	38
β-strand	1225-1234	10	33
β-strand	1235	1	27
α-helix	1239-1241	3
β-strand	1244-1246	3	39
β-strand	1251	1	40
α-helix	1257	1
β-strand	1258	1	40
α-helix	1259	1
α-helix	1266-1267	2
β-strand	1268-1270	3	41
α-helix	1272-1281	10
α-helix	1284-1291	8
α-helix	1292-1296	5
α-helix	1298-1309	12
α-helix	1321-1332	12
β-strand	1335-1340	6	42

Chain J: 74 helices, 82 β-strands

Element	Residues	Length	Sheet
β-strand	19-24	6	42
α-helix	27-33	7
β-strand	34-37	4	43
β-strand	44	1	44
α-helix	50	1
β-strand	51	1	44
α-helix	52	1
α-helix	59-62	4
α-helix	78-80	3
α-helix	83	1
β-strand	84	1	45
α-helix	85	1
β-strand	91	1	45
α-helix	95-99	5
β-strand	102-112	11	43
α-helix	115-118	4
α-helix	122	1
α-helix	123-128	6
α-helix	132-139	8
β-strand	144-148	5	46
β-strand	159-160	2	46
α-helix	162-172	11
β-strand	177-179	3	46
α-helix	181-191	11
α-helix	194-207	14
α-helix	212-229	18
α-helix	234-237	4
β-strand	238-244	7	43
α-helix	247-249	3
β-strand	254-255	2	47
β-strand	259-260	2	47
α-helix	264-285	22
α-helix	289-307	19
α-helix	315-316	2
β-strand	317-319	3	48
β-strand	322-323	2	48
α-helix	328-330	3
α-helix	337	1
α-helix	338-342	5
β-strand	345-347	3	41
β-strand	350-354	5	39
β-strand	355-357	3	49
β-strand	365-369	5	49
α-helix	370-376	7
α-helix	378-387	10
α-helix	394-402	9
α-helix	406-415	10
β-strand	421-424	4	39
α-helix	431-433	3
β-strand	434-437	4	39
β-strand	438-442	5	49
β-strand	447-449	3	49
α-helix	451-453	3
α-helix	454-457	4
β-strand	465-469	5	39
α-helix	474-482	9
β-strand	485	1	39
α-helix	486-488	3
β-strand	491	1	50
β-strand	498	1	50
α-helix	505-513	9
β-strand	526-527	2	51
α-helix	530-539	10
β-strand	547-557	11	51
β-strand	563-573	11	51
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	615-635	21
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	52
β-strand	713-717	5	52
α-helix	721-727	7
α-helix	734-741	8
β-strand	745	1	53
β-strand	748	1	54
α-helix	753	1
β-strand	754	1	54
α-helix	755	1
β-strand	759	1	53
α-helix	769-804	36
β-strand	809-811	3	55
β-strand	820-822	3	56
β-strand	825-826	2	57
β-strand	831-833	3	57
α-helix	835-839	5
β-strand	843	1	58
β-strand	844	1	56
β-strand	848-849	2	59
β-strand	856-858	3	59
β-strand	863	1	58
α-helix	866-874	9
β-strand	880-882	3	56
α-helix	885-887	3
β-strand	894-895	2	55
α-helix	896-899	4
β-strand	901	1	60
β-strand	908	1	60
α-helix	909-910	2
α-helix	915-924	10
α-helix	925-929	5
β-strand	949-952	4	61
β-strand	956-961	6	62
β-strand	965-967	3	61
β-strand	973-975	3	61
β-strand	980-985	6	62
β-strand	991-997	7	62
β-strand	1002-1003	2	61
β-strand	1010-1011	2	62
β-strand	1015-1019	5	61
β-strand	1024-1028	5	63
β-strand	1033	1	64
β-strand	1034-1038	5	65
β-strand	1042	1	63
β-strand	1046-1051	6	63
β-strand	1056-1061	6	63
α-helix	1069-1072	4
β-strand	1077-1081	5	65
α-helix	1086	1
β-strand	1087	1	65
α-helix	1088	1
β-strand	1089	1	66
α-helix	1090	1
β-strand	1096	1	66
β-strand	1098-1100	3	65
β-strand	1106-1107	2	63
β-strand	1115	1	64
β-strand	1120-1125	6	63
α-helix	1138-1146	9
α-helix	1148-1150	3
α-helix	1153-1154	2
β-strand	1155-1156	2	67
β-strand	1161-1165	5	68
β-strand	1172-1178	7	68
β-strand	1186-1191	6	68
β-strand	1203-1204	2	68
β-strand	1209-1211	3	67
α-helix	1214-1216	3
α-helix	1217-1224	8
α-helix	1226-1242	17
α-helix	1250-1259	10
β-strand	1263-1268	6	69
β-strand	1279-1281	3	69
α-helix	1282-1294	13
β-strand	1301-1305	5	69
α-helix	1309-1314	6
α-helix	1319-1325	7
α-helix	1328-1338	11
β-strand	1341-1342	2	42
α-helix	1347-1352	6
α-helix	1361-1371	11

Chain K: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-13	7
α-helix	16-31	16
α-helix	46-56	11
α-helix	61-79	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA non-template strand	A	DNA	62	Escherichia coli
DNA template strand	B	DNA	62	Escherichia coli
DNA-directed RNA polymerase subunit alpha	G, H	protein	329	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	91	Escherichia coli	P0A800 (AlphaFold model)
RNA scaffold	R	RNA	31	Escherichia coli

Sequence of entity 1 (A), FASTA

>12EC_1 DNA non-template strand (chains A)
GCGTGCAAGGAGGTTGTATGGAACTCGTAATCATGCACCCGTAAATTCACCGGTTCAGAC
CG

Sequence of entity 2 (B), FASTA

>12EC_2 DNA template strand (chains B)
CGGTCTGAACCGGTGAATTTACGGGTGCAACTATACGAGTTCCATACAACCTCCTTGCAC
GC

Sequence of entity 3 (G, H), FASTA

>12EC_3 DNA-directed RNA polymerase subunit alpha (chains G, H)
MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE
IDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGD
VEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPV
ERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP
EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL
TEIKDVLASRGLSLGMRLENWPPASIADE

Sequence of entity 4 (I), FASTA

>12EC_4 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 5 (J), FASTA

>12EC_5 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 6 (K), FASTA

>12EC_6 DNA-directed RNA polymerase subunit omega (chains K)
MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLIN
NQILDVRERQEQQEQEAAELQAVTAIAEGRR

Sequence of entity 7 (R), FASTA

>12EC_7 RNA scaffold (chains R)
GCGGUCUAGUCUUACCGCGAGGUAUAGUUGC

Ligands and cofactors

ID	Name	Formula	Copies
1N7	Chapso	C32 H59 N2 O8 S	1
MG	Magnesium ion	Mg	1
ZN	Zinc ion	Zn	2

Primary citation

ppGpp regulates transcription elongation via direct and indirect inputs to RNA polymerase pausing and nucleotide addition. Mueller, A.U., Mooney, R.A., Engstrom, M.D. et al. bioRxiv (2026). DOI 10.64898/2026.05.13.724835 · 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
9ZP4 2.42 Å, E. coli RNA polymerase elongation complex containing the unnatural dZ:PTP base pair in a…
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…
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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