6N58: Escherichia coli RNAP polymerase

Cryo-EM structure of Escherichia coli RNAP polymerase bound with TraR in conformation II. Determined by electron microscopy at 3.78 Å resolution. Released 26 Feb 2020.

Method: Electron microscopy
Resolution: 3.78 Å
Organism: Escherichia coli
Chains: 7
Atoms: 30,189
Mol. weight: 473.92 kDa
Ligands: ZN, MG, 1N7
Released: 26 Feb 2020

Explore 6N58 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6N58 contains 168 α-helices and 215 β-strands across 7 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: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	13-17	5	1
β-strand	23-32	10	1
α-helix	35-49	15
β-strand	53	1	2
β-strand	56-59	4	3
β-strand	74	1	4
α-helix	78-85	8
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
α-helix	155-158	4
β-strand	171-172	2	3
α-helix	173-175	3
β-strand	180-185	6	1
β-strand	188-189	2	1
β-strand	198-207	10	1
α-helix	213-233	21

Chain H: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	6
β-strand	23-24	2	7
β-strand	25	1	6
β-strand	27-31	5	8
α-helix	35-49	15
β-strand	53-61	9	9
β-strand	74	1	10
α-helix	78-85	8
β-strand	99-101	3	9
β-strand	104-105	2	11
α-helix	112-114	3
β-strand	133	1	10
β-strand	139-140	2	11
β-strand	142-149	8	9
β-strand	153	1	12
β-strand	172	1	9
β-strand	175	1	12
β-strand	180-183	4	7
β-strand	186-190	5	8
β-strand	198-202	5	8
β-strand	205-207	3	7
α-helix	213-227	15

Chain I: 56 helices, 100 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	13	1	13
α-helix	19-20	2
α-helix	23-25	3
α-helix	29-38	10
α-helix	49-56	8
α-helix	57	1
β-strand	59-60	2	14
β-strand	66-69	4	14
β-strand	73-75	3	14
α-helix	76-78	3
α-helix	82-88	7
β-strand	95	1	15
β-strand	96-105	10	14
α-helix	106	1
β-strand	114-122	9	14
β-strand	126	1	15
β-strand	136-137	2	16
β-strand	142-144	3	16
α-helix	146	1
β-strand	147-148	2	17
β-strand	149-150	2	18
α-helix	151-152	2
β-strand	154-158	5	19
β-strand	173-177	5	19
β-strand	180	1	20
β-strand	184-188	5	19
β-strand	194-198	5	19
β-strand	204-205	2	19
α-helix	207-212	6
α-helix	217-223	7
β-strand	227-231	5	21
β-strand	238-240	3	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	292-294	3
β-strand	296-297	2	21
β-strand	301-302	2	24
β-strand	309-311	3	24
β-strand	315-316	2	21
α-helix	319-326	8
β-strand	332-336	5	21
α-helix	347-353	7
α-helix	359-370	12
α-helix	378-389	12
β-strand	396	1	20
α-helix	399-407	9
α-helix	422-437	16
α-helix	448-450	3
β-strand	452-453	2	18
α-helix	456-480	25
α-helix	495-507	13
β-strand	513-514	2	16
α-helix	520-526	7
β-strand	530-531	2	17
β-strand	535	1	25
β-strand	537	1	25
α-helix	545-548	4
α-helix	552-554	3
β-strand	580-581	2	26
β-strand	587-588	2	26
β-strand	589-594	6	27
β-strand	598	1	28
β-strand	599-606	8	27
β-strand	616-617	2	27
β-strand	623	1	29
β-strand	628	1	28
β-strand	629	1	29
β-strand	633-637	5	27
β-strand	642-646	5	27
β-strand	652-653	2	27
α-helix	671-673	3
α-helix	676-686	11
β-strand	689	1	30
α-helix	690-691	2
α-helix	704-711	8
β-strand	716-717	2	31
β-strand	722-726	5	32
β-strand	731-736	6	32
β-strand	749-752	4	32
β-strand	758	1	33
β-strand	764	1	33
β-strand	768-769	2	31
α-helix	772	1
β-strand	776-777	2	32
β-strand	782-785	4	31
β-strand	789-790	2	34
β-strand	793-794	2	34
β-strand	798-804	7	35
β-strand	816	1	36
β-strand	818	1	37
α-helix	821-824	4
β-strand	830-832	3	38
β-strand	835-838	4	39
β-strand	841	1	40
β-strand	842-843	2	41
β-strand	846-847	2	41
α-helix	848	1
β-strand	849	1	42
β-strand	865	1	43
β-strand	870	1	44
β-strand	871	1	43
α-helix	872	1
β-strand	882-884	3	44
β-strand	887-889	3	42
α-helix	899-906	8
β-strand	913-915	3	42
β-strand	918-919	2	44
α-helix	920-921	2
β-strand	922	1	45
β-strand	924	1	45
β-strand	928-935	8	39
β-strand	936	1	46
α-helix	943-980	38
α-helix	1006-1037	32
α-helix	1039	1
β-strand	1040	1	46
β-strand	1046	1	40
β-strand	1048-1054	7	39
β-strand	1056-1058	3	38
β-strand	1065-1067	3	47
β-strand	1073-1075	3	47
β-strand	1076	1	36
β-strand	1087-1088	2	48
α-helix	1092	1
β-strand	1093	1	48
α-helix	1094	1
β-strand	1096	1	37
α-helix	1100-1102	3
α-helix	1110-1133	24
α-helix	1139-1150	12
α-helix	1161-1163	3
α-helix	1166-1176	11
β-strand	1182	1	13
α-helix	1186-1188	3
α-helix	1192-1201	10
β-strand	1212-1213	2	48
β-strand	1220	1	48
α-helix	1221	1
β-strand	1226-1232	7	35
β-strand	1235	1	30
α-helix	1239-1242	4
β-strand	1244-1246	3	49
β-strand	1251	1	50
β-strand	1258	1	50
β-strand	1270	1	51
α-helix	1273-1280	8
α-helix	1285-1290	6
α-helix	1300-1309	10
α-helix	1321-1332	12
β-strand	1335-1339	5	52

Chain J: 64 helices, 79 β-strands

Element	Residues	Length	Sheet
β-strand	20-24	5	52
α-helix	27-33	7
β-strand	44	1	53
β-strand	51	1	53
α-helix	52	1
α-helix	78-80	3
α-helix	83	1
β-strand	84	1	54
α-helix	85	1
β-strand	91	1	54
α-helix	95-99	5
β-strand	103-112	10	55
α-helix	114-116	3
α-helix	123-128	6
α-helix	132-140	9
β-strand	145-146	2	56
β-strand	159	1	56
α-helix	162-171	10
β-strand	178-179	2	56
α-helix	182-191	10
α-helix	194-206	13
α-helix	211-229	19
α-helix	235-237	3
β-strand	238-244	7	55
α-helix	245	1
β-strand	252-254	3	57
β-strand	260-262	3	57
α-helix	265-285	21
α-helix	289-307	19
α-helix	327-329	3
α-helix	337-341	5
β-strand	345	1	51
β-strand	350-352	3	49
β-strand	353-354	2	58
β-strand	365-369	5	59
α-helix	370-376	7
α-helix	378-388	11
α-helix	394-403	10
α-helix	406-415	10
β-strand	421-424	4	49
β-strand	434-437	4	49
β-strand	438-442	5	59
α-helix	451-453	3
α-helix	454-457	4
β-strand	465-466	2	58
β-strand	467-469	3	49
α-helix	474-482	9
β-strand	485	1	49
α-helix	486-488	3
β-strand	491	1	60
β-strand	498	1	60
α-helix	505-513	9
β-strand	517	1	61
β-strand	526	1	62
α-helix	530-537	8
β-strand	546	1	61
β-strand	548-550	3	62
β-strand	553	1	63
β-strand	556	1	64
β-strand	564	1	64
β-strand	567	1	63
β-strand	570-572	3	62
α-helix	574-580	7
α-helix	589-591	3
α-helix	599-612	14
α-helix	615-635	21
α-helix	641-643	3
α-helix	650-669	20
α-helix	675-701	27
β-strand	706-707	2	65
β-strand	714-715	2	65
α-helix	721-727	7
α-helix	734-740	7
α-helix	769-788	20
α-helix	790-792	3
α-helix	795-801	7
β-strand	811	1	66
β-strand	820-822	3	67
β-strand	825	1	68
β-strand	833	1	68
α-helix	835-838	4
α-helix	843	1
β-strand	844	1	67
β-strand	848	1	69
β-strand	858	1	69
α-helix	866-874	9
β-strand	880-882	3	67
β-strand	895	1	66
α-helix	897-899	3
α-helix	915-924	10
α-helix	926-929	4
β-strand	949-950	2	70
β-strand	956	1	71
β-strand	957-961	5	72
β-strand	966-967	2	73
β-strand	973-974	2	73
β-strand	981-985	5	72
β-strand	991-996	6	72
α-helix	997-998	2
β-strand	1002	1	70
β-strand	1011	1	71
β-strand	1018-1019	2	70
β-strand	1025-1026	2	74
β-strand	1033	1	75
β-strand	1034-1038	5	76
β-strand	1042	1	77
β-strand	1046	1	77
β-strand	1050	1	78
β-strand	1057	1	78
α-helix	1060	1
β-strand	1061	1	79
α-helix	1062	1
α-helix	1069-1071	3
β-strand	1077-1081	5	76
α-helix	1087-1088	2
β-strand	1089	1	80
α-helix	1090	1
β-strand	1096	1	80
β-strand	1098-1100	3	76
β-strand	1105	1	79
β-strand	1106-1107	2	74
β-strand	1115	1	75
β-strand	1122-1124	3	74
α-helix	1139-1145	7
β-strand	1156	1	81
β-strand	1161-1165	5	82
β-strand	1173-1179	7	82
β-strand	1186-1190	5	82
β-strand	1204	1	82
α-helix	1205	1
β-strand	1209	1	81
α-helix	1217-1223	7
α-helix	1226-1244	19
α-helix	1250-1260	11
β-strand	1263-1268	6	83
β-strand	1279-1281	3	83
α-helix	1282-1294	13
β-strand	1301-1304	4	83
α-helix	1309-1312	4
α-helix	1319-1325	7
α-helix	1328-1338	11
α-helix	1348-1352	5
α-helix	1362-1372	11

Chain K: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-12	6
α-helix	18-31	14
α-helix	46-55	10
α-helix	61-79	19

Chain L: 30 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	8-19	12
α-helix	24-29	6
α-helix	38-50	13
α-helix	77-89	13
α-helix	97-106	10
α-helix	116-135	20
α-helix	138-150	13
α-helix	151-155	5
α-helix	214-232	19
α-helix	245-256	12
α-helix	263-291	29
α-helix	300-306	7
α-helix	317-320	4
α-helix	330-333	4
α-helix	334-351	18
α-helix	355-391	37
α-helix	392-394	3
α-helix	401-417	17
α-helix	421-423	3
α-helix	427-445	19
α-helix	454-473	20
α-helix	480-486	7
α-helix	493-500	8
α-helix	503-504	2
β-strand	505-506	2	57
α-helix	519-521	3
α-helix	531-549	19
α-helix	553-562	10
α-helix	573-579	7
α-helix	585-599	15
α-helix	605-609	5

Chain M: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	4-26	23
α-helix	42-45	4
α-helix	46-51	6
α-helix	59-70	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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 polymerase sigma factor RpoD	L	protein	616	Escherichia coli	P00579
Protein TraR	M	protein	72	Escherichia coli	P41065

Sequence of entity 1 (G, H), FASTA

>6N58_1 DNA-directed RNA polymerase subunit alpha (chains G, H)
MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE
IDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGD
VEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPV
ERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP
EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL
TEIKDVLASRGLSLGMRLENWPPASIADE

Sequence of entity 2 (I), FASTA

>6N58_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

>6N58_3 DNA-directed RNA polymerase subunit beta' (chains J)
VKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCAR
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

>6N58_4 DNA-directed RNA polymerase subunit omega (chains K)
MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLIN
NQILDVRERQEQQEQEAAELQAVTAIAEGRR

Sequence of entity 5 (L), FASTA

>6N58_5 RNA polymerase sigma factor RpoD (chains L)
SEFMEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVME
EAPDADDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEI
DIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPT
ATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKA
KGRSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKM
PKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQ
VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD
KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE
PTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATT
ESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRK
LRHPSRSEVLRSFLDD

Sequence of entity 6 (M), FASTA

>6N58_6 Protein TraR (chains M)
SDEADEAYSVTEQLTMTGINRIRQKINAHGIPVYLCEACGNPIPEARRKIFPGVTLCVEC
QAYQERQRKHYA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3
MG	Magnesium ion	Mg	1
1N7	Chapso	C32 H59 N2 O8 S	4

Primary citation

E. coliTraR allosterically regulates transcription initiation by altering RNA polymerase conformation. Chen, J., Gopalkrishnan, S., Chiu, C. et al. Elife (2019) 8. DOI 10.7554/eLife.49375 · 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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