6N57: Escherichia coli RNAP polymerase

Cryo-EM structure of Escherichia coli RNAP polymerase bound with TraR in conformation I. Determined by electron microscopy at 3.7 Å resolution. Released 26 Feb 2020.

Method: Electron microscopy
Resolution: 3.7 Å
Organism: Escherichia coli
Chains: 7
Atoms: 30,233
Mol. weight: 473.92 kDa
Ligands: 1N7, ZN, MG
Released: 26 Feb 2020

Explore 6N57 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6N57 contains 157 α-helices and 212 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: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	14-17	4	1
β-strand	23-27	5	1
α-helix	35-49	15
β-strand	53	1	2
β-strand	56	1	3
β-strand	61	1	4
β-strand	74	1	5
α-helix	78-85	8
β-strand	97	1	6
β-strand	102-105	4	4
β-strand	108-111	4	5
α-helix	112-114	3
β-strand	129-133	5	5
β-strand	139-142	4	4
β-strand	146	1	3
β-strand	147	1	6
β-strand	149	1	2
α-helix	173-175	3
β-strand	180-182	3	1
β-strand	185	1	1
β-strand	188-189	2	7
β-strand	199-200	2	7
β-strand	202-207	6	1
α-helix	213-233	21

Chain H: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	16-17	2	8
β-strand	23-24	2	9
β-strand	25-26	2	8
β-strand	31	1	10
α-helix	35-49	15
β-strand	53-61	9	11
β-strand	71	1	12
β-strand	74	1	12
α-helix	78-86	9
β-strand	90	1	13
β-strand	99	1	11
β-strand	104-105	2	14
β-strand	109	1	15
α-helix	112-114	3
β-strand	123	1	13
β-strand	132	1	15
β-strand	133	1	12
β-strand	139-140	2	14
β-strand	142-149	8	11
β-strand	152-153	2	16
β-strand	175-176	2	16
β-strand	183	1	9
β-strand	187-190	4	10
β-strand	198-201	4	10
β-strand	205-206	2	9
α-helix	213-227	15
α-helix	228-230	3

Chain I: 46 helices, 97 β-strands

Element	Residues	Length	Sheet
β-strand	13-14	2	17
α-helix	23-25	3
α-helix	29-38	10
α-helix	49-56	8
β-strand	66-69	4	18
β-strand	73-75	3	19
α-helix	76-78	3
α-helix	82-87	6
β-strand	95-98	4	19
β-strand	101-104	4	18
α-helix	105-106	2
β-strand	116-119	4	18
β-strand	122-126	5	19
α-helix	128-130	3
β-strand	136-137	2	20
β-strand	142-144	3	20
α-helix	145-146	2
β-strand	147	1	21
β-strand	150-151	2	22
α-helix	152	1
β-strand	155-157	3	23
β-strand	174-176	3	23
β-strand	180	1	24
β-strand	184-188	5	23
β-strand	194-198	5	23
β-strand	204-205	2	23
α-helix	207-212	6
α-helix	217-221	5
β-strand	227-231	5	25
β-strand	238-239	2	25
β-strand	250	1	26
β-strand	255-257	3	27
β-strand	260-263	4	27
β-strand	268	1	26
α-helix	271-278	8
α-helix	289-292	4
β-strand	297	1	25
β-strand	301-302	2	28
β-strand	309-311	3	28
β-strand	315	1	25
α-helix	319-326	8
β-strand	333-336	4	25
α-helix	347-353	7
α-helix	359-370	12
α-helix	374-376	3
α-helix	378-388	11
β-strand	396	1	24
α-helix	399-408	10
α-helix	422-437	16
β-strand	451-452	2	22
α-helix	456-478	23
α-helix	495-507	13
β-strand	513-514	2	20
α-helix	520-524	5
β-strand	530	1	21
α-helix	545-547	3
β-strand	580-581	2	29
β-strand	587-588	2	29
β-strand	589	1	30
β-strand	591-594	4	31
β-strand	599-603	5	31
β-strand	606	1	30
β-strand	616	1	31
β-strand	623	1	32
β-strand	629	1	32
β-strand	633-637	5	31
β-strand	642-646	5	31
α-helix	647-649	3
β-strand	652-654	3	31
α-helix	671-673	3
α-helix	676-686	11
β-strand	689	1	33
β-strand	700-701	2	17
α-helix	705-710	6
β-strand	717	1	34
β-strand	722-727	6	35
β-strand	732-736	5	35
β-strand	757-758	2	36
β-strand	764-765	2	36
β-strand	768-769	2	37
β-strand	776-777	2	35
β-strand	782	1	34
β-strand	784-785	2	37
β-strand	789-790	2	38
β-strand	793-794	2	38
β-strand	798-802	5	39
β-strand	803-804	2	40
β-strand	816	1	41
β-strand	819	1	42
α-helix	820-824	5
β-strand	832-833	2	43
β-strand	836-838	3	44
β-strand	841	1	45
β-strand	842-843	2	46
β-strand	846-847	2	46
α-helix	848	1
β-strand	849	1	47
β-strand	865	1	48
β-strand	871	1	48
β-strand	882-884	3	49
β-strand	887-889	3	47
α-helix	899-906	8
β-strand	913-915	3	47
β-strand	918-919	2	49
α-helix	920-921	2
β-strand	930-933	4	44
β-strand	936	1	50
α-helix	943-979	37
α-helix	1006-1037	32
β-strand	1040	1	50
β-strand	1046	1	45
β-strand	1050-1053	4	44
β-strand	1055-1056	2	43
β-strand	1065	1	51
β-strand	1068	1	39
β-strand	1075	1	51
β-strand	1076	1	41
β-strand	1080	1	42
β-strand	1087-1088	2	52
β-strand	1097-1098	2	40
α-helix	1100-1102	3
α-helix	1110-1133	24
α-helix	1138-1150	13
α-helix	1166-1176	11
β-strand	1182-1183	2	17
α-helix	1192-1200	9
β-strand	1209-1210	2	53
β-strand	1212-1213	2	52
β-strand	1220	1	52
α-helix	1221	1
β-strand	1225-1226	2	53
β-strand	1228-1232	5	39
β-strand	1235	1	33
α-helix	1239-1242	4
β-strand	1244-1246	3	54
β-strand	1252	1	55
β-strand	1270	1	56
α-helix	1272-1280	9
α-helix	1285-1288	4
α-helix	1289-1293	5
α-helix	1300-1309	10
α-helix	1322-1332	11
β-strand	1335-1339	5	57

Chain J: 62 helices, 72 β-strands

Element	Residues	Length	Sheet
β-strand	20-24	5	57
α-helix	27-32	6
β-strand	44	1	58
β-strand	51	1	58
α-helix	52	1
α-helix	78-80	3
α-helix	83	1
β-strand	84	1	59
α-helix	85	1
β-strand	91	1	59
α-helix	96-99	4
β-strand	103-112	10	60
α-helix	115-118	4
α-helix	125-128	4
α-helix	132-140	9
β-strand	145-146	2	61
β-strand	159	1	61
α-helix	162-171	10
β-strand	178-179	2	61
α-helix	182-191	10
α-helix	194-206	13
α-helix	211-229	19
α-helix	234-237	4
β-strand	238-244	7	60
α-helix	245	1
β-strand	252-254	3	62
β-strand	260-262	3	62
α-helix	265-285	21
α-helix	289-307	19
α-helix	323-325	3
α-helix	337-341	5
β-strand	345	1	56
β-strand	350-352	3	54
β-strand	355	1	63
β-strand	365-369	5	64
α-helix	370-376	7
α-helix	378-387	10
α-helix	394-403	10
α-helix	406-415	10
α-helix	420	1
β-strand	421-424	4	65
β-strand	434-437	4	65
β-strand	438-442	5	64
β-strand	447	1	63
α-helix	453-457	5
β-strand	467-469	3	65
α-helix	475-482	8
α-helix	486-488	3
β-strand	491	1	66
β-strand	498	1	66
α-helix	505-513	9
β-strand	517	1	67
α-helix	530-539	10
β-strand	546	1	67
β-strand	548-549	2	68
β-strand	553-556	4	69
β-strand	564-567	4	69
β-strand	571-572	2	68
α-helix	574-580	7
α-helix	589-591	3
α-helix	598-612	15
α-helix	615-635	21
α-helix	645-647	3
α-helix	650-668	19
α-helix	675-701	27
β-strand	706-707	2	70
β-strand	714-715	2	70
α-helix	721-727	7
α-helix	734-740	7
β-strand	748	1	71
α-helix	753	1
β-strand	754	1	71
α-helix	755	1
α-helix	769-786	18
α-helix	788-791	4
α-helix	795-803	9
β-strand	820-822	3	72
β-strand	825	1	73
β-strand	833	1	73
β-strand	843	1	74
β-strand	844	1	72
β-strand	848	1	75
β-strand	858	1	75
β-strand	863	1	74
α-helix	866-874	9
β-strand	880-882	3	72
α-helix	885-887	3
α-helix	915-924	10
α-helix	926-929	4
β-strand	936	1	76
β-strand	949-951	3	77
β-strand	957-961	5	78
β-strand	965-967	3	77
β-strand	973-975	3	77
β-strand	981-985	5	78
β-strand	991-996	6	78
β-strand	1002-1003	2	77
β-strand	1016-1019	4	77
β-strand	1025	1	79
β-strand	1036	1	80
β-strand	1042	1	81
β-strand	1046-1049	4	81
β-strand	1058-1061	4	81
α-helix	1062	1
α-helix	1071-1073	3
β-strand	1077-1079	3	80
α-helix	1088	1
β-strand	1089	1	82
α-helix	1090	1
β-strand	1096	1	82
β-strand	1098-1100	3	80
β-strand	1124	1	79
β-strand	1135	1	76
α-helix	1139-1146	8
β-strand	1156	1	83
β-strand	1161-1165	5	84
β-strand	1170	1	84
β-strand	1172-1178	7	84
β-strand	1187-1191	5	84
β-strand	1203-1204	2	84
α-helix	1205	1
β-strand	1209	1	83
α-helix	1214-1216	3
α-helix	1217-1223	7
α-helix	1226-1244	19
α-helix	1250-1260	11
β-strand	1263-1266	4	85
β-strand	1279-1281	3	85
α-helix	1282-1294	13
β-strand	1302-1304	3	85
α-helix	1309-1312	4
α-helix	1328-1338	11
α-helix	1348-1353	6
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: 32 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	8-19	12
α-helix	24-30	7
α-helix	32	1
α-helix	40-50	11
α-helix	77-89	13
α-helix	98-105	8
α-helix	116-136	21
α-helix	138-153	16
α-helix	158-161	4
α-helix	214-232	19
α-helix	245-256	12
α-helix	263-295	33
α-helix	299-306	8
α-helix	314-320	7
α-helix	326-328	3
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	451-452	2
α-helix	454-473	20
α-helix	480-486	7
α-helix	493-500	8
β-strand	505-506	2	62
α-helix	519-522	4
β-strand	524	1	55
α-helix	528-530	3
α-helix	531-549	19
α-helix	553-561	9
α-helix	573-580	8
α-helix	585-599	15
α-helix	605-609	5

Chain M: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	6-26	21
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

>6N57_1 DNA-directed RNA polymerase subunit alpha (chains G, H)
MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE
IDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGD
VEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPV
ERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP
EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL
TEIKDVLASRGLSLGMRLENWPPASIADE

Sequence of entity 2 (I), FASTA

>6N57_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

>6N57_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

>6N57_4 DNA-directed RNA polymerase subunit omega (chains K)
MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLIN
NQILDVRERQEQQEQEAAELQAVTAIAEGRR

Sequence of entity 5 (L), FASTA

>6N57_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

>6N57_6 Protein TraR (chains M)
SDEADEAYSVTEQLTMTGINRIRQKINAHGIPVYLCEACGNPIPEARRKIFPGVTLCVEC
QAYQERQRKHYA

Ligands and cofactors

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

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…

Browse structure collections

About this viewer

MolViewer shows 6N57 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.