6N61: DNA-directed RNA polymerase subunit alpha

Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA and Capistruin. Determined by X-ray diffraction at 3.25 Å resolution. Released 9 Jan 2019.

Method: X-ray diffraction
Resolution: 3.25 Å
Organisms: Escherichia coli, Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264)
Chains: 9
Atoms: 28,590
Mol. weight: 458.57 kDa
Ligands: ZN, MG
Released: 9 Jan 2019

Explore 6N61 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6N61 contains 158 α-helices and 199 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: 8 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	13-17	5	1
β-strand	23-28	6	1
α-helix	35-47	13
β-strand	54-61	8	2
β-strand	71	1	3
β-strand	74	1	3
α-helix	78-86	9
β-strand	90-91	2	4
β-strand	98-105	8	2
β-strand	108-111	4	3
α-helix	112-114	3
β-strand	115-116	2	2
α-helix	117	1
β-strand	122-123	2	4
β-strand	129-133	5	3
β-strand	139-148	10	2
β-strand	151-153	3	5
α-helix	155-158	4
β-strand	171-172	2	2
β-strand	175-177	3	5
β-strand	180-189	10	1
β-strand	199-207	9	1
α-helix	213-227	15
α-helix	228-231	4

Chain B: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	13-17	5	6
β-strand	23-28	6	6
α-helix	35-49	15
β-strand	52-60	9	7
β-strand	74	1	8
α-helix	78-87	10
β-strand	90	1	9
β-strand	98-101	4	7
β-strand	108-110	3	8
β-strand	123	1	9
β-strand	131-133	3	8
β-strand	143-150	8	7
β-strand	152-153	2	10
β-strand	172	1	7
β-strand	175-176	2	10
β-strand	180-190	11	6
β-strand	198-207	10	6
α-helix	213-228	16

Chain C: 60 helices, 92 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
α-helix	11-12	2
β-strand	13-14	2	11
α-helix	15	1
α-helix	19-20	2
α-helix	23-25	3
α-helix	29-39	11
α-helix	49-56	8
β-strand	59-60	2	12
β-strand	67-75	9	12
α-helix	76-78	3
α-helix	82-88	7
β-strand	93-105	13	12
β-strand	115-128	14	12
β-strand	130	1	13
β-strand	136-137	2	13
β-strand	142-145	4	13
β-strand	147-151	5	14
β-strand	154-158	5	15
β-strand	173-177	5	15
β-strand	180	1	16
β-strand	184-188	5	15
β-strand	194-198	5	15
β-strand	205	1	15
α-helix	207-212	6
α-helix	217-224	8
α-helix	226	1
β-strand	227-231	5	17
β-strand	238-240	3	17
α-helix	245-247	3
α-helix	250-251	2
α-helix	271-279	9
β-strand	284-286	3	17
α-helix	289-292	4
β-strand	296-297	2	17
β-strand	301-302	2	18
β-strand	309-311	3	18
β-strand	315-316	2	17
α-helix	319-327	9
β-strand	333-336	4	17
α-helix	346-351	6
α-helix	359-370	12
α-helix	378-390	13
β-strand	396	1	16
α-helix	399-408	10
α-helix	422-437	16
α-helix	442-444	3
α-helix	448-450	3
β-strand	451-454	4	14
α-helix	456-470	15
α-helix	472-480	9
α-helix	495-507	13
β-strand	509	1	13
β-strand	512-514	3	13
α-helix	520-527	8
β-strand	529	1	19
β-strand	530-531	2	14
α-helix	550-551	2
α-helix	552-554	3
β-strand	558	1	20
α-helix	573	1
β-strand	574	1	19
β-strand	575	1	20
β-strand	576	1	21
β-strand	580-581	2	22
β-strand	587-594	8	22
β-strand	598	1	23
β-strand	599-607	9	22
α-helix	608-613	6
β-strand	616	1	22
β-strand	628	1	23
β-strand	633-637	5	22
β-strand	642-646	5	22
β-strand	652-654	3	22
β-strand	662	1	21
α-helix	663-666	4
α-helix	671-673	3
α-helix	676-687	12
β-strand	689	1	24
α-helix	690-692	3
β-strand	700-701	2	11
α-helix	705-709	5
β-strand	716-717	2	25
β-strand	722-727	6	26
β-strand	731-736	6	26
β-strand	748-752	5	26
β-strand	757-758	2	27
β-strand	763	1	28
β-strand	764-765	2	27
β-strand	768-769	2	25
β-strand	776-777	2	26
β-strand	782-785	4	25
β-strand	789-790	2	29
β-strand	793-794	2	29
β-strand	798-804	7	30
β-strand	816-819	4	30
α-helix	820-824	5
β-strand	830-841	12	28
β-strand	849	1	31
α-helix	859-862	4
β-strand	865	1	32
β-strand	870	1	33
β-strand	871	1	32
α-helix	872	1
β-strand	876	1	28
β-strand	882-884	3	33
β-strand	887	1	31
β-strand	889	1	34
α-helix	897-905	9
β-strand	913	1	34
β-strand	918-919	2	33
α-helix	920-921	2
β-strand	927-935	9	28
α-helix	940-941	2
α-helix	943-979	37
α-helix	986-989	4
α-helix	994-999	6
α-helix	1008-1037	30
α-helix	1039-1040	2
β-strand	1046-1058	13	28
β-strand	1065-1067	3	35
β-strand	1073-1075	3	35
β-strand	1076-1080	5	30
β-strand	1087	1	36
β-strand	1093	1	36
β-strand	1096-1098	3	30
α-helix	1102-1105	4
α-helix	1110-1133	24
α-helix	1138-1149	12
α-helix	1168-1174	7
β-strand	1182-1183	2	11
α-helix	1192-1201	10
β-strand	1209-1210	2	37
β-strand	1213	1	36
α-helix	1219	1
β-strand	1220	1	36
α-helix	1221	1
β-strand	1225-1226	2	37
β-strand	1227-1232	6	30
β-strand	1233-1234	2	35
β-strand	1235	1	24
β-strand	1244-1246	3	38
β-strand	1251	1	39
β-strand	1252	1	40
β-strand	1258	1	39
α-helix	1266-1267	2
β-strand	1268-1270	3	41
α-helix	1272-1280	9
α-helix	1284-1291	8
α-helix	1298-1309	12
α-helix	1321-1331	11
β-strand	1335-1339	5	42

Chain D: 58 helices, 68 β-strands

Element	Residues	Length	Sheet
β-strand	20-24	5	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
β-strand	84	1	45
β-strand	91	1	45
α-helix	95-99	5
β-strand	102-112	11	43
α-helix	115-118	4
α-helix	123-127	5
α-helix	132-139	8
β-strand	144-147	4	46
β-strand	159-160	2	46
α-helix	162-166	5
β-strand	177-179	3	46
α-helix	182-190	9
α-helix	194-206	13
α-helix	212-215	4
α-helix	217-230	14
α-helix	234-237	4
β-strand	238-244	7	43
α-helix	247-249	3
α-helix	253	1
β-strand	254	1	47
α-helix	255	1
β-strand	260	1	47
β-strand	261-262	2	48
α-helix	264-285	22
α-helix	289-307	19
β-strand	316	1	49
β-strand	323	1	49
α-helix	324-325	2
α-helix	328-330	3
α-helix	338-342	5
β-strand	345-347	3	41
β-strand	350-354	5	38
β-strand	355-357	3	50
β-strand	365-369	5	50
α-helix	370-376	7
α-helix	378-387	10
α-helix	394-403	10
α-helix	406-416	11
β-strand	421-425	5	38
α-helix	431-433	3
β-strand	434-437	4	38
β-strand	438-442	5	50
α-helix	446	1
β-strand	447-449	3	50
α-helix	451-457	7
β-strand	465-469	5	38
α-helix	474-482	9
β-strand	485	1	38
β-strand	491	1	51
β-strand	498	1	51
α-helix	505-514	10
α-helix	530-538	9
β-strand	549-558	10	52
β-strand	562-571	10	52
α-helix	574-579	6
α-helix	598-612	15
α-helix	614-635	22
α-helix	650-670	21
α-helix	675-702	28
β-strand	706-709	4	53
β-strand	712-715	4	53
α-helix	721-728	8
α-helix	734-741	8
α-helix	769-804	36
β-strand	809-811	3	54
β-strand	820-822	3	55
β-strand	825-827	3	56
β-strand	828	1	57
β-strand	830-833	4	56
α-helix	835-839	5
β-strand	843	1	58
β-strand	844	1	55
α-helix	848-850	3
β-strand	863	1	58
α-helix	866-874	9
β-strand	880-882	3	55
β-strand	894-895	2	54
α-helix	896-899	4
β-strand	901	1	59
β-strand	908	1	59
α-helix	909-910	2
α-helix	915-924	10
α-helix	926-929	4
β-strand	936	1	60
β-strand	950	1	61
β-strand	957-961	5	62
β-strand	965-967	3	63
β-strand	973-975	3	63
β-strand	981-984	4	62
β-strand	985	1	64
β-strand	991	1	64
β-strand	994	1	57
β-strand	995-996	2	62
β-strand	1003	1	63
β-strand	1009-1010	2	62
β-strand	1018	1	61
α-helix	1138-1145	8
α-helix	1148-1150	3
α-helix	1153-1155	3
β-strand	1156	1	65
β-strand	1162	1	66
β-strand	1164-1165	2	67
β-strand	1175-1176	2	67
β-strand	1187-1188	2	67
β-strand	1203	1	66
β-strand	1209	1	65
α-helix	1217-1224	8
α-helix	1226-1243	18
α-helix	1250-1260	11
β-strand	1263-1266	4	68
β-strand	1279-1281	3	68
α-helix	1282-1294	13
β-strand	1302-1305	4	68
α-helix	1309-1314	6
α-helix	1319-1325	7
α-helix	1328-1337	10
β-strand	1341-1342	2	42
α-helix	1348-1352	5
α-helix	1361-1371	11

Chain E: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-12	6
α-helix	16-31	16
α-helix	46-56	11
α-helix	61-74	14

Chain F: 25 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	97-102	6
α-helix	105-107	3
α-helix	109-110	2
α-helix	114-135	22
α-helix	263-288	26
α-helix	289-293	5
α-helix	299-306	8
α-helix	314-321	8
α-helix	327-351	25
α-helix	355-391	37
α-helix	401-417	17
α-helix	421-423	3
α-helix	427-446	20
α-helix	454-469	16
α-helix	471-474	4
α-helix	480-486	7
α-helix	492-500	9
α-helix	502-504	3
β-strand	505-506	2	48
β-strand	510-511	2	69
α-helix	512-514	3
β-strand	515-518	4	69
β-strand	524	1	40
α-helix	529-530	2
α-helix	531-548	18
α-helix	553-562	10
α-helix	573-578	6
α-helix	584-599	16
α-helix	605-608	4

Chain I: 0 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	70
β-strand	12	1	60
β-strand	13-14	2	70

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	90	Escherichia coli	P0A800 (AlphaFold model)
RNA polymerase sigma factor RpoD	F	protein	613	Escherichia coli	Q0P6L9
non-template strand DNA	N	DNA	29	Escherichia coli
template strand DNA	T	DNA	24	Escherichia coli
Capistruin	I	protein	19	Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264)	A0A096YQF1

Sequence of entity 1 (A, B), FASTA

>6N61_1 DNA-directed RNA polymerase subunit alpha (chains A, B)
MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE
IDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGD
VEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPV
ERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLEVLFQ

Sequence of entity 2 (C), FASTA

>6N61_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

>6N61_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

>6N61_4 DNA-directed RNA polymerase subunit omega (chains E)
MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLIN
NQILDVRERQEQQEQEAAELQAVTAIAEGR

Sequence of entity 5 (F), FASTA

>6N61_5 RNA polymerase sigma factor RpoD (chains F)
MEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAP
DADDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA
KRIEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLITGFVDPNAEEDLAPTATH
VGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGR
SHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKK
NFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKD
INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE
YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP
EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESL
RAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRH
PSRSEVLRSFLDD

Sequence of entity 6 (N), FASTA

>6N61_6 non-template strand DNA (chains N)
GACCTTCCCCTGATGGGAAGGTTTATAAT

Sequence of entity 7 (T), FASTA

>6N61_7 template strand DNA (chains T)
AAACCTTCCCATCAGGGGAAGGTC

Sequence of entity 8 (I), FASTA

>6N61_8 Capistruin (chains I)
GTPGFQTPDARVISRFGFN

Ligands and cofactors

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

Water and common crystallization additives (EDO, EPE) are not listed.

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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