6N60: DNA-directed RNA polymerase subunit alpha

Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA and Microcin J25 (MccJ25). Determined by X-ray diffraction at 3.68 Å resolution. Released 9 Jan 2019.

Method: X-ray diffraction
Resolution: 3.68 Å
Organism: Escherichia coli
Chains: 9
Atoms: 27,705
Mol. weight: 458.37 kDa
Ligands: MG, ZN
Released: 9 Jan 2019

Explore 6N60 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6N60 contains 158 α-helices and 205 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 A: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	1
β-strand	24-31	8	1
α-helix	35-49	15
β-strand	53	1	2
β-strand	56-60	5	3
α-helix	78-86	9
β-strand	90-91	2	4
β-strand	97-104	8	3
β-strand	108-110	3	5
α-helix	112-114	3
β-strand	115	1	3
α-helix	116-117	2
β-strand	122-123	2	4
β-strand	131-133	3	5
β-strand	140-147	8	3
β-strand	149	1	2
β-strand	153	1	6
β-strand	170-172	3	3
β-strand	175	1	6
β-strand	180	1	7
β-strand	184-189	6	1
β-strand	199-204	6	1
β-strand	207	1	7
α-helix	213-227	15
α-helix	228-230	3

Chain B: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	12-13	2	8
β-strand	19	1	8
β-strand	23-31	9	8
α-helix	32	1
α-helix	35-49	15
β-strand	53-59	7	9
α-helix	78-86	9
β-strand	90-92	3	9
β-strand	98-103	6	9
β-strand	110-111	2	10
β-strand	115	1	9
β-strand	121-123	3	9
β-strand	129-131	3	10
β-strand	141-149	9	9
β-strand	153	1	11
α-helix	155-157	3
β-strand	172	1	9
β-strand	175	1	11
β-strand	180-190	11	8
β-strand	198-207	10	8
α-helix	213-228	16

Chain C: 63 helices, 95 β-strands

Element	Residues	Length	Sheet
β-strand	13-14	2	12
β-strand	16	1	13
α-helix	23-26	4
α-helix	29-38	10
α-helix	49-56	8
α-helix	57	1
β-strand	59-60	2	14
β-strand	67-75	9	14
α-helix	76-78	3
α-helix	82-88	7
β-strand	93-104	12	14
β-strand	116-128	13	14
β-strand	130	1	15
β-strand	136-137	2	15
β-strand	142-145	4	15
α-helix	146-147	2
β-strand	149-151	3	16
α-helix	152	1
β-strand	154-158	5	17
α-helix	164-166	3
α-helix	169-171	3
β-strand	173-177	5	17
β-strand	180	1	18
β-strand	184-187	4	17
β-strand	195-198	4	17
β-strand	204-205	2	17
α-helix	207-212	6
α-helix	217-224	8
β-strand	227-231	5	19
β-strand	238-239	2	19
β-strand	249	1	20
α-helix	257-259	3
β-strand	264	1	21
β-strand	267	1	21
β-strand	269	1	20
α-helix	271-279	9
β-strand	285-286	2	19
α-helix	292-294	3
β-strand	297	1	22
β-strand	301-302	2	23
β-strand	309-311	3	23
β-strand	315	1	22
α-helix	319-327	9
β-strand	332-336	5	19
α-helix	346-352	7
α-helix	359-370	12
α-helix	378-389	12
β-strand	396	1	18
α-helix	399-408	10
α-helix	422-436	15
α-helix	448-450	3
β-strand	451-453	3	16
α-helix	456-481	26
α-helix	489-492	4
α-helix	495-507	13
β-strand	512-514	3	15
α-helix	520-527	8
α-helix	550-551	2
α-helix	552-554	3
β-strand	558	1	24
α-helix	573-574	2
β-strand	575	1	24
β-strand	576	1	25
β-strand	580-581	2	26
β-strand	587-594	8	26
β-strand	599-607	9	26
α-helix	608-613	6
β-strand	616	1	26
β-strand	623	1	27
β-strand	629	1	27
β-strand	633-637	5	26
β-strand	642-646	5	26
β-strand	652-654	3	26
β-strand	662	1	25
α-helix	663-666	4
α-helix	671-673	3
β-strand	674	1	28
α-helix	676-685	10
α-helix	686-688	3
β-strand	689	1	29
α-helix	690-692	3
β-strand	700-701	2	12
α-helix	705-711	7
β-strand	716-717	2	30
β-strand	722-727	6	31
β-strand	731-736	6	31
α-helix	737	1
β-strand	749-752	4	31
β-strand	757-758	2	32
β-strand	763	1	33
β-strand	764-765	2	32
β-strand	768-769	2	30
β-strand	776-777	2	31
β-strand	782-785	4	30
β-strand	789-790	2	34
β-strand	793-794	2	34
β-strand	798-804	7	35
β-strand	816-819	4	35
α-helix	820-825	6
β-strand	830-841	12	33
β-strand	842-843	2	36
β-strand	846-847	2	36
β-strand	849	1	37
β-strand	865	1	38
β-strand	870	1	39
β-strand	871	1	38
α-helix	872	1
β-strand	876-877	2	33
β-strand	882-884	3	39
β-strand	887-889	3	37
α-helix	897-906	10
β-strand	913-915	3	37
β-strand	918-919	2	39
α-helix	920-921	2
β-strand	926-935	10	33
α-helix	940-942	3
α-helix	943-980	38
α-helix	988-991	4
α-helix	994-997	4
α-helix	1008-1037	30
α-helix	1039-1041	3
β-strand	1046-1058	13	33
α-helix	1059-1060	2
β-strand	1065	1	40
β-strand	1066-1067	2	41
β-strand	1075	1	40
β-strand	1076-1080	5	35
α-helix	1082-1084	3
β-strand	1087	1	42
β-strand	1093	1	42
β-strand	1096-1098	3	35
α-helix	1102-1106	5
β-strand	1108	1	28
α-helix	1110-1133	24
α-helix	1138-1149	12
β-strand	1155	1	13
α-helix	1166-1176	11
β-strand	1182-1183	2	12
α-helix	1189-1191	3
α-helix	1192-1201	10
β-strand	1209-1210	2	35
β-strand	1213	1	42
α-helix	1219	1
β-strand	1220	1	42
α-helix	1221	1
β-strand	1225-1232	8	35
β-strand	1233-1234	2	41
β-strand	1235	1	29
α-helix	1239-1242	4
β-strand	1244-1246	3	43
β-strand	1252	1	44
β-strand	1270	1	45
α-helix	1272-1280	9
α-helix	1285-1288	4
α-helix	1289-1293	5
α-helix	1298-1310	13
α-helix	1321-1332	12
β-strand	1335-1339	5	46

Chain D: 59 helices, 69 β-strands

Element	Residues	Length	Sheet
β-strand	20-24	5	46
α-helix	25-26	2
α-helix	27-33	7
β-strand	34-37	4	47
β-strand	44	1	48
α-helix	50	1
β-strand	51	1	48
α-helix	52	1
α-helix	83	1
β-strand	84	1	49
α-helix	85	1
β-strand	91	1	49
α-helix	95-99	5
β-strand	102-112	11	47
α-helix	114-118	5
α-helix	123-127	5
α-helix	132-139	8
β-strand	144-147	4	50
β-strand	159-160	2	50
α-helix	162-168	7
β-strand	177-179	3	50
α-helix	182-191	10
α-helix	194-207	14
α-helix	211-230	20
α-helix	234-237	4
β-strand	238-244	7	47
α-helix	247-249	3
β-strand	254	1	51
α-helix	256-258	3
β-strand	260	1	51
β-strand	261-262	2	52
α-helix	264-284	21
α-helix	289-307	19
β-strand	316	1	53
β-strand	323	1	53
α-helix	324-325	2
α-helix	327-331	5
α-helix	338-343	6
β-strand	345	1	45
β-strand	350-354	5	43
β-strand	355-356	2	54
β-strand	365-369	5	54
α-helix	370-376	7
α-helix	378-387	10
α-helix	394-403	10
α-helix	408-416	9
β-strand	421-425	5	43
α-helix	431-433	3
β-strand	434-437	4	43
β-strand	438-442	5	54
β-strand	447-448	2	54
α-helix	451-457	7
β-strand	465-469	5	43
α-helix	474-482	9
β-strand	485	1	43
β-strand	491	1	55
β-strand	498	1	55
α-helix	505-513	9
β-strand	526-527	2	56
α-helix	530-538	9
β-strand	547-558	12	56
β-strand	562-573	12	56
α-helix	574-580	7
α-helix	589-592	4
α-helix	598-612	15
α-helix	614-635	22
α-helix	649-669	21
α-helix	675-702	28
β-strand	706-707	2	57
β-strand	714-715	2	57
α-helix	721-727	7
α-helix	734-741	8
β-strand	748	1	58
α-helix	753	1
β-strand	754	1	58
α-helix	755	1
α-helix	769-803	35
β-strand	809-811	3	59
β-strand	820-822	3	60
β-strand	825-826	2	61
β-strand	830	1	62
β-strand	831-833	3	61
α-helix	835-839	5
β-strand	843	1	63
β-strand	844	1	60
β-strand	849	1	64
β-strand	856	1	64
β-strand	863	1	63
α-helix	866-875	10
β-strand	880-882	3	60
β-strand	894-895	2	59
α-helix	896-899	4
α-helix	908-910	3
α-helix	915-928	14
β-strand	950	1	65
β-strand	956-961	6	62
β-strand	965-967	3	65
β-strand	973-975	3	65
β-strand	981-985	5	62
β-strand	991-996	6	62
α-helix	997-998	2
β-strand	1002-1003	2	65
β-strand	1010-1011	2	62
β-strand	1018-1019	2	65
α-helix	1139-1145	7
α-helix	1148-1150	3
β-strand	1156	1	66
β-strand	1161-1162	2	67
β-strand	1164-1165	2	68
β-strand	1170	1	69
β-strand	1172	1	69
β-strand	1173-1176	4	68
β-strand	1187-1190	4	68
β-strand	1203-1204	2	67
β-strand	1209	1	66
α-helix	1217-1223	7
α-helix	1226-1243	18
α-helix	1250-1260	11
β-strand	1263-1268	6	70
β-strand	1279-1281	3	70
α-helix	1282-1294	13
β-strand	1301-1304	4	70
α-helix	1309-1312	4
α-helix	1319-1324	6
α-helix	1328-1337	10
β-strand	1341-1342	2	46
α-helix	1348-1353	6
α-helix	1361-1370	10

Chain E: 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	61-77	17

Chain F: 21 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	97-107	11
α-helix	114-132	19
α-helix	138-143	6
α-helix	264-271	8
α-helix	355-391	37
α-helix	401-418	18
α-helix	421-423	3
α-helix	427-446	20
α-helix	454-469	16
α-helix	482-486	5
α-helix	493-499	7
α-helix	503-504	2
β-strand	505-506	2	52
α-helix	509	1
β-strand	510	1	71
α-helix	511	1
β-strand	518	1	71
α-helix	519-522	4
β-strand	524	1	44
α-helix	529-530	2
α-helix	531-550	20
α-helix	553-562	10
α-helix	573-580	8
α-helix	585-599	15
α-helix	605-609	5

Chain M: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	72
β-strand	19-20	2	72

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA-directed RNA polymerase subunit alpha	A, B	protein	239	Escherichia coli	P0A7Z4 (AlphaFold model)
DNA-directed RNA polymerase subunit beta	C	protein	1342	Escherichia coli	P0A8V2 (AlphaFold model)
DNA-directed RNA polymerase subunit beta'	D	protein	1409	Escherichia coli	P0A8T7 (AlphaFold model)
DNA-directed RNA polymerase subunit omega	E	protein	91	Escherichia coli	P0A800 (AlphaFold model)
RNA polymerase sigma factor RpoD	F	protein	612	Escherichia coli	Q0P6L9
Microcin J25	M	protein	21	Escherichia coli	Q9X2V7
non-template strand DNA	N	DNA	29	Escherichia coli
template strand DNA	T	DNA	24	Escherichia coli

Sequence of entity 1 (A, B), FASTA

>6N60_1 DNA-directed RNA polymerase subunit alpha (chains A, B)
MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE
IDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGD
VEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPV
ERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLEVLFQ

Sequence of entity 2 (C), FASTA

>6N60_2 DNA-directed RNA polymerase subunit beta (chains C)
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 (D), FASTA

>6N60_3 DNA-directed RNA polymerase subunit beta' (chains D)
VKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCAR
IFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSL
PSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDEFDAKM
GAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILT
VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQ
EAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPY
LRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHP
VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA
RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSG
LASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKA
ISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAE
VAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFN
SIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGAR
KGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVL
GRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYG
RDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKL
SNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANW
DPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKI
VDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDITGGLPR
VADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFE
GERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQM
LRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFI
SAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAGEAPA
APQVTAEDASASLAELLNAGLGGSDNELE

Sequence of entity 4 (E), FASTA

>6N60_4 DNA-directed RNA polymerase subunit omega (chains E)
MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLIN
NQILDVRERQEQQEQEAAELQAVTAIAEGRR

Sequence of entity 5 (F), FASTA

>6N60_5 RNA polymerase sigma factor RpoD (chains F)
MEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAP
DADDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA
KRIEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLITGFVDPNAEEDLAPTATH
VGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGR
SHATAQEEILKLSEVFKQFRLVPKQFDYVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKN
FITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDI
NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY
RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE
ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR
AATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHP
SRSEVLRSFLDD

Sequence of entity 6 (M), FASTA

>6N60_6 Microcin J25 (chains M)
GGAGHVPEYFVGIGTPISFYG

Sequence of entity 7 (N), FASTA

>6N60_7 non-template strand DNA (chains N)
GACCTTCCCCTGATGGGAAGGTTTATAAT

Sequence of entity 8 (T), FASTA

>6N60_8 template strand DNA (chains T)
AAACCTTCCCATCAGGGGAAGGTC

Ligands and cofactors

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

Primary citation

Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin. Braffman, N.R., Piscotta, F.J., Hauver, J. et al. Proc Natl Acad Sci U S A (2019) 116:1273-1278. DOI 10.1073/pnas.1817352116 · 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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