6C6S: E.coli RNA polymerase elongation complex

CryoEM structure of E.coli RNA polymerase elongation complex bound with RfaH. Determined by electron microscopy at 3.7 Å resolution. Released 25 Jul 2018.

Method: Electron microscopy
Resolution: 3.7 Å
Organisms: Escherichia coli, Escherichia coli (strain K12)
Chains: 9
Atoms: 27,691
Mol. weight: 412.19 kDa
Ligands: MG, ZN
Released: 25 Jul 2018

Explore 6C6S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6C6S contains 142 α-helices and 237 β-strands across 6 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 D: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	85
α-helix	14-23	10
β-strand	27-29	3	85
β-strand	32-38	7	86
β-strand	43-49	7	86
β-strand	54-59	6	85
α-helix	66-70	5
β-strand	75-78	4	85
α-helix	85-89	5
α-helix	90-95	6
α-helix	110-111	2
β-strand	115-118	4	87
α-helix	121-123	3
β-strand	128-130	3	87
β-strand	139-143	5	87
β-strand	150-154	5	87
β-strand	159-161	3	87

Chain G: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	1
β-strand	24-31	8	1
α-helix	35-49	15
β-strand	53	1	2
β-strand	56-61	6	3
β-strand	74	1	4
α-helix	78-86	9
β-strand	90-91	2	5
β-strand	97-105	9	3
β-strand	108-111	4	4
α-helix	112-114	3
β-strand	115	1	3
β-strand	122-123	2	5
β-strand	129-133	5	4
β-strand	139-147	9	3
β-strand	149	1	2
β-strand	153	1	6
α-helix	155-158	4
β-strand	171-172	2	3
α-helix	173-174	2
β-strand	175	1	6
β-strand	180-189	10	1
β-strand	192	1	7
β-strand	195	1	7
β-strand	199-207	9	1
α-helix	213-229	17

Chain H: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	12-16	5	8
β-strand	23-31	9	8
α-helix	35-49	15
β-strand	52-61	10	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	108-110	3	10
α-helix	112-114	3
β-strand	121-123	3	11
β-strand	131-133	3	10
β-strand	139-150	12	9
β-strand	152-153	2	12
β-strand	170-172	3	9
α-helix	173-174	2
β-strand	175-176	2	12
β-strand	180-185	6	8
β-strand	188	1	13
β-strand	199	1	8
β-strand	200	1	13
β-strand	201-207	7	8
α-helix	213-226	14

Chain I: 57 helices, 100 β-strands

Element	Residues	Length	Sheet
α-helix	11-12	2
β-strand	13-14	2	14
α-helix	19-20	2
α-helix	29-38	10
α-helix	43-45	3
α-helix	49-56	8
β-strand	59-60	2	15
β-strand	67-75	9	15
α-helix	82-88	7
β-strand	93-104	12	15
α-helix	113-114	2
β-strand	116-128	13	15
β-strand	143-145	3	16
α-helix	146	1
β-strand	147-148	2	17
β-strand	150-151	2	18
α-helix	152	1
β-strand	154-158	5	19
β-strand	173-177	5	19
β-strand	180	1	20
β-strand	184-187	4	19
β-strand	195-197	3	19
β-strand	204-205	2	19
α-helix	208-212	5
α-helix	217-224	8
β-strand	227-231	5	21
β-strand	239-240	2	21
α-helix	243-246	4
β-strand	250	1	22
β-strand	255-257	3	23
β-strand	260-263	4	23
β-strand	268	1	22
α-helix	271-280	10
β-strand	284-285	2	21
α-helix	289-291	3
β-strand	296-297	2	21
β-strand	301-303	3	24
β-strand	308-311	4	24
β-strand	315-316	2	21
α-helix	319-328	10
β-strand	332-336	5	21
β-strand	339	1	25
β-strand	343	1	25
α-helix	346-353	8
α-helix	359-370	12
α-helix	375-376	2
α-helix	378-388	11
β-strand	396	1	20
α-helix	399-407	9
α-helix	422-437	16
α-helix	442-444	3
β-strand	451-452	2	18
α-helix	456-479	24
α-helix	496-507	12
β-strand	512-514	3	16
α-helix	520-527	8
β-strand	529	1	26
β-strand	530-531	2	17
α-helix	552-554	3
β-strand	558	1	27
α-helix	573	1
β-strand	574	1	26
β-strand	575	1	27
β-strand	580-581	2	28
β-strand	587-588	2	28
β-strand	589-593	5	29
α-helix	600	1
β-strand	603-606	4	29
α-helix	608-611	4
β-strand	616-617	2	29
β-strand	623	1	30
β-strand	629	1	30
β-strand	633-637	5	29
β-strand	642-646	5	29
β-strand	652-654	3	29
α-helix	671-673	3
β-strand	674	1	31
α-helix	676-686	11
β-strand	689	1	32
α-helix	690-691	2
β-strand	692	1	33
β-strand	696	1	34
β-strand	700-701	2	14
α-helix	705-711	7
β-strand	717	1	35
β-strand	722-727	6	36
β-strand	731-736	6	36
α-helix	737	1
β-strand	748-752	5	36
β-strand	757-758	2	37
β-strand	763	1	33
β-strand	764-765	2	37
β-strand	768-769	2	38
β-strand	776-777	2	36
β-strand	782	1	35
β-strand	784-785	2	38
β-strand	789-790	2	39
β-strand	793-794	2	39
β-strand	798-804	7	34
β-strand	816-818	3	34
α-helix	820-824	5
β-strand	830-832	3	33
β-strand	835-841	7	40
β-strand	849	1	41
α-helix	859-862	4
β-strand	865	1	42
β-strand	870	1	43
β-strand	871	1	42
α-helix	872	1
β-strand	882-884	3	43
β-strand	887-888	2	41
α-helix	897-905	9
β-strand	914-915	2	41
β-strand	918-919	2	43
α-helix	920-921	2
β-strand	930-935	6	40
α-helix	943-978	36
α-helix	1006-1037	32
α-helix	1039-1041	3
β-strand	1046-1053	8	40
β-strand	1056-1058	3	33
β-strand	1065-1067	3	32
β-strand	1073-1075	3	32
β-strand	1076-1079	4	34
β-strand	1087	1	44
β-strand	1088	1	45
α-helix	1092	1
β-strand	1093	1	44
α-helix	1094	1
β-strand	1096-1098	3	34
α-helix	1100-1102	3
β-strand	1108	1	31
α-helix	1110-1133	24
α-helix	1138-1150	13
α-helix	1161-1163	3
α-helix	1168-1176	9
β-strand	1182-1183	2	14
α-helix	1192-1201	10
β-strand	1209-1210	2	46
β-strand	1212	1	45
β-strand	1213	1	47
β-strand	1220	1	47
α-helix	1221	1
β-strand	1225-1226	2	46
β-strand	1227-1232	6	34
β-strand	1233-1235	3	32
α-helix	1239-1242	4
β-strand	1244-1246	3	48
β-strand	1251	1	49
β-strand	1258	1	49
β-strand	1268-1270	3	50
α-helix	1272-1280	9
α-helix	1284-1288	5
α-helix	1289-1293	5
α-helix	1298-1309	12
α-helix	1321-1331	11
β-strand	1335-1339	5	51

Chain J: 63 helices, 88 β-strands

Element	Residues	Length	Sheet
β-strand	20-24	5	51
α-helix	27-33	7
β-strand	37	1	52
β-strand	44	1	53
β-strand	51	1	53
α-helix	52	1
α-helix	78-80	3
β-strand	84	1	54
α-helix	85	1
β-strand	91	1	54
α-helix	95-99	5
β-strand	103-112	10	52
α-helix	114-117	4
α-helix	132-139	8
β-strand	145-146	2	55
β-strand	159	1	55
α-helix	162-171	10
β-strand	178-179	2	55
α-helix	181-190	10
α-helix	194-206	13
α-helix	211-229	19
α-helix	234-236	3
β-strand	238-244	7	52
α-helix	247-249	3
β-strand	253-254	2	56
β-strand	260-261	2	56
α-helix	264-285	22
α-helix	289-307	19
β-strand	317	1	57
β-strand	323	1	57
α-helix	324	1
α-helix	327-331	5
α-helix	338-342	5
β-strand	345-347	3	50
β-strand	350-354	5	48
β-strand	355-356	2	58
β-strand	366-369	4	58
α-helix	370-376	7
α-helix	378-388	11
α-helix	394-403	10
α-helix	408-416	9
β-strand	421-425	5	48
α-helix	431-433	3
β-strand	434-437	4	48
β-strand	439-442	4	58
β-strand	447-448	2	58
α-helix	451-453	3
α-helix	454-457	4
β-strand	465-469	5	48
α-helix	474-482	9
β-strand	485	1	48
β-strand	491	1	59
β-strand	498	1	59
α-helix	505-513	9
β-strand	526	1	60
α-helix	530-539	10
β-strand	547-549	3	60
β-strand	552-556	5	61
β-strand	564-568	5	61
β-strand	571-573	3	60
α-helix	574-580	7
α-helix	589-591	3
α-helix	599-612	14
α-helix	615-635	21
α-helix	645-647	3
α-helix	650-670	21
α-helix	675-702	28
β-strand	706-708	3	62
β-strand	713-715	3	62
α-helix	721-727	7
α-helix	734-741	8
β-strand	748	1	63
α-helix	753	1
β-strand	754	1	63
α-helix	755	1
α-helix	766-767	2
α-helix	769-804	36
β-strand	809-811	3	64
α-helix	820	1
β-strand	821-822	2	65
β-strand	825-826	2	66
β-strand	831-833	3	66
α-helix	835-838	4
β-strand	843	1	67
β-strand	844	1	68
α-helix	847	1
β-strand	848-850	3	69
β-strand	855-858	4	69
β-strand	863	1	67
α-helix	866-875	10
β-strand	880-881	2	65
β-strand	882	1	68
β-strand	894-895	2	64
α-helix	896-899	4
β-strand	901	1	70
β-strand	908	1	70
α-helix	909-910	2
α-helix	915-924	10
α-helix	925-927	3
β-strand	951	1	71
β-strand	957-961	5	72
β-strand	965-967	3	73
β-strand	973-975	3	73
β-strand	980-985	6	72
β-strand	991-997	7	72
β-strand	1003	1	73
β-strand	1016	1	71
β-strand	1029	1	74
β-strand	1033	1	75
β-strand	1034-1038	5	76
β-strand	1042	1	77
β-strand	1046-1049	4	77
β-strand	1058-1061	4	77
α-helix	1062-1063	2
β-strand	1077-1081	5	76
β-strand	1087	1	76
β-strand	1089	1	78
α-helix	1090	1
β-strand	1091	1	79
β-strand	1093	1	79
β-strand	1096	1	78
β-strand	1098-1100	3	76
β-strand	1105-1106	2	77
α-helix	1114	1
β-strand	1115	1	75
β-strand	1117	1	74
α-helix	1138-1146	9
β-strand	1156	1	80
β-strand	1161-1165	5	81
β-strand	1170	1	82
β-strand	1172	1	82
β-strand	1173-1178	6	81
β-strand	1187-1190	4	81
β-strand	1196	1	83
β-strand	1203-1204	2	81
β-strand	1209	1	80
β-strand	1211	1	83
α-helix	1217-1219	3
α-helix	1220-1224	5
α-helix	1226-1243	18
α-helix	1251-1260	10
β-strand	1263-1268	6	84
β-strand	1279-1281	3	84
α-helix	1282-1293	12
β-strand	1301-1304	4	84
α-helix	1309-1312	4
α-helix	1319-1323	5
α-helix	1328-1337	10
β-strand	1341-1342	2	51
α-helix	1348-1353	6
α-helix	1362-1371	10

Chain K: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	7-12	6
α-helix	18-31	14
α-helix	46-55	10
α-helix	61-77	17
α-helix	79-83	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (29-mer)	A	DNA	29	Escherichia coli
DNA (29-mer)	B	DNA	29	Escherichia coli
RNA (5'-r(gpcpapupupcpapapapgpcpcpgpapgpapgpgpupa)-3')	R	RNA	20	Escherichia coli
DNA-directed RNA polymerase subunit alpha	G, H	protein	239	Escherichia coli (strain K12)	P0A7Z4 (AlphaFold model)
DNA-directed RNA polymerase subunit beta	I	protein	1342	Escherichia coli (strain K12)	P0A8V2 (AlphaFold model)
DNA-directed RNA polymerase subunit beta'	J	protein	1407	Escherichia coli (strain K12)	P0A8T7 (AlphaFold model)
DNA-directed RNA polymerase subunit omega	K	protein	91	Escherichia coli	P0A800 (AlphaFold model)
Transcription antitermination protein RfaH	D	protein	162	Escherichia coli (strain K12)	P0AFW0

Sequence of entity 1 (A), FASTA

>6C6S_1 DNA (29-MER) (chains A)
GGGCTGCGGTAGCGTGACGGCGAATACCC

Sequence of entity 2 (B), FASTA

>6C6S_2 DNA (29-MER) (chains B)
GGGTATTCGCCGTGTACCTCTCGCAGCCC

Sequence of entity 3 (R), FASTA

>6C6S_3 RNA (5'-R(*GP*CP*AP*UP*UP*CP*AP*AP*AP*GP*CP*CP*GP*AP*GP*AP*GP*GP*UP*A)-3') (chains R)
GCAUUCAAAGCCGAGAGGUA

Sequence of entity 4 (G, H), FASTA

>6C6S_4 DNA-directed RNA polymerase subunit alpha (chains G, H)
MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE
IDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGD
VEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPV
ERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLEVLFQ

Sequence of entity 5 (I), FASTA

>6C6S_5 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 6 (J), FASTA

>6C6S_6 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
APQVTAEDASASLAELLNAGLGGSDNE

Sequence of entity 7 (K), FASTA

>6C6S_7 DNA-directed RNA polymerase subunit omega (chains K)
MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLIN
NQILDVRERQEQQEQEAAELQAVTAIAEGRR

Sequence of entity 8 (D), FASTA

>6C6S_8 Transcription antitermination protein RfaH (chains D)
MQSWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFD
PEVIHTTTINATRGVSHFVRFGASPAIVPSAVIHQLSVYKPKDIVDPATPYPGDKVIITE
GAFEGFQAIFTEPDGEARSMLLLNLINKEIKHSVKNTEFRKL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
ZN	Zinc ion	Zn	2

Primary citation

Structural Basis for Transcript Elongation Control by NusG Family Universal Regulators. Kang, J.Y., Mooney, R.A., Nedialkov, Y. et al. Cell (2018) 173:1650-1662.e14. DOI 10.1016/j.cell.2018.05.017 · 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…
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…

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