8HKC: E. coli RNAP sigma32 complex

Cryo-EM structure of E. coli RNAP sigma32 complex. Determined by electron microscopy at 2.49 Å resolution. Released 31 May 2023.

Method: Electron microscopy
Resolution: 2.49 Å
Organisms: Escherichia coli K-12, Escherichia coli
Chains: 7
Atoms: 25,779
Mol. weight: 448.5 kDa
Ligands: MG, ZN
Released: 31 May 2023

Explore 8HKC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8HKC contains 164 α-helices and 182 β-strands across 5 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, 17 β-strands

Element	Residues	Length	Sheet
β-strand	15-20	6	1
β-strand	23-28	6	1
α-helix	35-49	15
β-strand	52-61	10	2
β-strand	74	1	3
α-helix	78-86	9
β-strand	89	1	2
β-strand	90-91	2	4
β-strand	97-105	9	2
β-strand	108-111	4	3
α-helix	112-114	3
β-strand	115	1	2
β-strand	122-123	2	4
β-strand	129-133	5	3
β-strand	139-150	12	2
β-strand	152-153	2	5
α-helix	155-160	6
α-helix	165-167	3
β-strand	170-172	3	2
β-strand	175-176	2	5
β-strand	180-192	13	1
β-strand	195-207	13	1
α-helix	213-227	15

Chain B: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	6
β-strand	23-28	6	6
α-helix	35-49	15
β-strand	52-61	10	7
β-strand	74	1	8
α-helix	78-86	9
β-strand	90-92	3	9
β-strand	97-105	9	7
β-strand	108-111	4	8
α-helix	112-114	3
β-strand	115	1	7
α-helix	116-117	2
β-strand	118	1	9
β-strand	121-123	3	9
β-strand	129-133	5	8
β-strand	139-150	12	7
β-strand	152-153	2	10
α-helix	155-158	4
β-strand	170-172	3	7
β-strand	175-176	2	10
β-strand	180-189	10	6
β-strand	199-207	9	6
α-helix	213-232	20

Chain C: 61 helices, 86 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
α-helix	11-12	2
β-strand	13-14	2	11
α-helix	23-26	4
α-helix	29-39	11
α-helix	49-56	8
β-strand	59-60	2	12
β-strand	66-75	10	12
α-helix	82-88	7
β-strand	93-106	14	12
β-strand	112-128	17	12
α-helix	129	1
β-strand	130	1	13
β-strand	136-138	3	13
β-strand	141-145	5	13
α-helix	146	1
β-strand	147-151	5	14
α-helix	152	1
β-strand	154-160	7	15
β-strand	171-177	7	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
β-strand	227-229	3	17
β-strand	334-336	3	17
α-helix	346-353	8
α-helix	359-370	12
α-helix	379-389	11
β-strand	396	1	16
α-helix	399-408	10
α-helix	422-436	15
α-helix	442-444	3
β-strand	451-454	4	14
α-helix	456-481	26
α-helix	489-491	3
α-helix	496-508	13
β-strand	512-514	3	13
α-helix	520-527	8
β-strand	529-531	3	14
α-helix	545-548	4
α-helix	552-554	3
β-strand	558	1	18
β-strand	572-574	3	14
β-strand	575	1	18
β-strand	580-581	2	19
β-strand	587-595	9	19
β-strand	598-607	10	19
α-helix	608-611	4
β-strand	616-617	2	19
β-strand	623	1	20
β-strand	628	1	19
β-strand	629	1	20
β-strand	633-638	6	19
β-strand	641-646	6	19
α-helix	647-649	3
β-strand	652-653	2	19
α-helix	665-667	3
α-helix	671-673	3
β-strand	674	1	21
α-helix	676-685	10
α-helix	686-688	3
β-strand	689	1	22
α-helix	690-691	2
β-strand	700-701	2	11
α-helix	705-712	8
β-strand	716-717	2	23
β-strand	722-727	6	24
β-strand	731-736	6	24
α-helix	738-740	3
β-strand	748-752	5	24
α-helix	753-754	2
β-strand	757-758	2	25
β-strand	763	1	26
β-strand	764-765	2	25
β-strand	768-769	2	23
β-strand	776-777	2	24
β-strand	782-785	4	23
β-strand	789-790	2	27
β-strand	793-794	2	27
β-strand	798-804	7	28
α-helix	812-814	3
β-strand	816-819	4	28
α-helix	820-824	5
β-strand	830-841	12	26
β-strand	842	1	29
β-strand	847	1	29
β-strand	849-850	2	30
α-helix	861-863	3
β-strand	865	1	31
β-strand	870	1	32
β-strand	871	1	31
α-helix	872	1
β-strand	876-877	2	26
β-strand	882-884	3	32
β-strand	886-889	4	30
α-helix	897-906	10
α-helix	908-910	3
β-strand	913-915	3	30
β-strand	918-919	2	32
α-helix	920-921	2
β-strand	926-935	10	26
β-strand	936	1	33
α-helix	940-941	2
α-helix	943-972	30
α-helix	1027-1037	11
α-helix	1038-1039	2
β-strand	1040	1	33
α-helix	1042-1043	2
β-strand	1046-1058	13	26
β-strand	1065-1067	3	34
β-strand	1073-1075	3	34
β-strand	1076-1080	5	28
α-helix	1082-1084	3
β-strand	1087	1	35
β-strand	1093	1	35
β-strand	1096-1098	3	28
α-helix	1102-1106	5
β-strand	1108	1	21
α-helix	1110-1133	24
α-helix	1138-1150	13
α-helix	1161-1163	3
α-helix	1166-1176	11
β-strand	1182-1183	2	11
α-helix	1192-1201	10
β-strand	1209-1210	2	36
β-strand	1213	1	35
α-helix	1219	1
β-strand	1220	1	35
α-helix	1221	1
β-strand	1225-1226	2	36
β-strand	1227-1232	6	28
β-strand	1233-1234	2	34
β-strand	1235	1	22
α-helix	1239-1241	3
β-strand	1244-1246	3	37
β-strand	1251-1252	2	38
β-strand	1268-1270	3	39
α-helix	1272-1281	10
α-helix	1284-1288	5
α-helix	1289-1293	5
α-helix	1298-1309	12
α-helix	1321-1332	12
β-strand	1335-1340	6	40
α-helix	1341	1

Chain E: 19 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	16-25	10
α-helix	27-30	4
α-helix	31-44	14
α-helix	47-56	10
α-helix	58-65	8
α-helix	66-71	6
α-helix	75-91	17
α-helix	95-97	3
α-helix	101-120	20
α-helix	130-142	13
α-helix	151-161	11
α-helix	165-176	12
α-helix	179	1
β-strand	180-181	2	45
α-helix	182	1
β-strand	202-203	2	38
α-helix	208-231	24
α-helix	234-240	7
α-helix	241-245	5
α-helix	253-260	8
α-helix	264-283	20

Chain F: 72 helices, 60 β-strands

Element	Residues	Length	Sheet
β-strand	19-24	6	40
α-helix	27-33	7
β-strand	37	1	41
β-strand	44	1	42
α-helix	50	1
β-strand	51	1	42
α-helix	52	1
α-helix	59-62	4
β-strand	84	1	43
β-strand	91	1	43
α-helix	95-99	5
β-strand	103-112	10	41
α-helix	115-118	4
α-helix	122	1
α-helix	123-128	6
α-helix	132-139	8
β-strand	144-148	5	44
β-strand	159-160	2	44
α-helix	162-172	11
β-strand	177-179	3	44
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	41
α-helix	247-249	3
β-strand	252-254	3	45
β-strand	260-262	3	45
α-helix	264-284	21
α-helix	289-307	19
α-helix	315-316	2
β-strand	317	1	46
α-helix	322	1
β-strand	323	1	46
α-helix	324-325	2
α-helix	327-330	4
α-helix	337	1
α-helix	338-342	5
β-strand	345-347	3	39
β-strand	350-354	5	37
β-strand	355-357	3	47
β-strand	365-369	5	47
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	37
α-helix	431-433	3
β-strand	434-437	4	37
β-strand	438-442	5	47
β-strand	447-449	3	47
α-helix	451-453	3
α-helix	454-457	4
β-strand	465-469	5	37
α-helix	474-479	6
α-helix	480-484	5
β-strand	485	1	37
α-helix	486-488	3
β-strand	491	1	48
β-strand	498	1	48
α-helix	505-513	9
β-strand	526-527	2	49
α-helix	530-538	9
β-strand	547-554	8	49
β-strand	557	1	50
β-strand	563	1	50
β-strand	566-573	8	49
α-helix	574-579	6
α-helix	580-582	3
α-helix	584	1
α-helix	589-591	3
α-helix	598-611	14
α-helix	615-635	21
α-helix	641-643	3
α-helix	645-647	3
α-helix	650-669	20
α-helix	675-702	28
β-strand	703-707	5	51
β-strand	713-717	5	51
α-helix	721-728	8
α-helix	734-741	8
β-strand	745	1	52
α-helix	746-747	2
β-strand	748	1	53
α-helix	749	1
α-helix	753	1
β-strand	754	1	53
α-helix	755	1
β-strand	759	1	52
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	830-833	4	56
α-helix	836-839	4
β-strand	843	1	57
β-strand	844	1	55
β-strand	863	1	57
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	58
β-strand	908	1	58
α-helix	909-910	2
α-helix	915-924	10
α-helix	925-929	5
α-helix	1138-1145	8
α-helix	1148-1150	3
α-helix	1153-1154	2
β-strand	1155-1156	2	59
β-strand	1161-1163	3	60
β-strand	1168	1	61
β-strand	1173	1	61
β-strand	1177-1178	2	60
β-strand	1203-1204	2	60
β-strand	1209-1210	2	59
α-helix	1217-1224	8
α-helix	1226-1243	18
α-helix	1250-1260	11
β-strand	1263-1268	6	62
β-strand	1279-1281	3	62
α-helix	1282-1292	11
α-helix	1294-1296	3
β-strand	1301-1304	4	62
α-helix	1309-1314	6
α-helix	1319-1325	7
α-helix	1328-1338	11
β-strand	1341-1343	3	40
α-helix	1347-1353	7
α-helix	1360-1362	3
α-helix	1363-1375	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA-directed RNA polymerase subunit alpha	A, B	protein	331	Escherichia coli K-12	P0A7Z4 (AlphaFold model)
DNA-directed RNA polymerase subunit beta	C	protein	1346	Escherichia coli K-12	P0A8V2 (AlphaFold model)
DNA-directed RNA polymerase subunit beta'	F	protein	1425	Escherichia coli K-12	P0A8T7 (AlphaFold model)
DNA (54-mer)	G	DNA	54	Escherichia coli
DNA (54-mer)	H	DNA	54	Escherichia coli
RNA polymerase sigma factor RpoH	E	protein	284	Escherichia coli K-12	P0AGB3 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8HKC_1 DNA-directed RNA polymerase subunit alpha (chains A, B)
MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE
IDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGD
VEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPV
ERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP
EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL
TEIKDVLASRGLSLGMRLENWPPASIADEKL

Sequence of entity 2 (C), FASTA

>8HKC_2 DNA-directed RNA polymerase subunit beta (chains C)
MEFVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFP
IQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIK
EQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIP
YRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQ
MELVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVA
KDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTND
RLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSG
ILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKER
LSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGL
TRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGV
VTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQ
QVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVA
KRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVE
RGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELAC
VSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPE
EKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKK
DLSEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQY
DELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISK
INPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEV
AKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKEL
LKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQP
LGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPG
MPESFNVLLKEIRSLGINIELEDESR

Sequence of entity 3 (F), FASTA

>8HKC_3 DNA-directed RNA polymerase subunit beta' (chains F)
MTSKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFC
ARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLK
SLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDEFDA
KMGAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMI
LTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRM
LQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVG
PYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIRE
HPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQL
EARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYR
SGLASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGK
KAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAE
AEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVS
FNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHG
ARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDR
VLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHC
YGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSI
KLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVA
NWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPAL
KIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDITGGL
PRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNV
FEGERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVR
QMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATES
FISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAGEA
PAAPQVTAEDASASLAELLNAGLGGSDNELEHHHHHHHHHHHHGT

Sequence of entity 4 (G), FASTA

>8HKC_4 DNA (54-MER) (chains G)
CCCCCTTGAAGACGTGGTTTACGACCCCATTTAGTAGTCAACCGCAGTGAGTGG

Sequence of entity 5 (H), FASTA

>8HKC_5 DNA (54-MER) (chains H)
CCACTCACTGCGGTTGACTACTAAATGGGGTCGTAAACCACGTCTTCAAGGGGG

Sequence of entity 6 (E), FASTA

>8HKC_6 RNA polymerase sigma factor RpoH (chains E)
MTDKMQSLALAPVGNLDSYIRAANAWPMLSADEERALAEKLHYHGDLEAAKTLILSHLRF
VVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN
WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDEVEMVARELGVTSKDVREMESRMAAQDM
TFDLSSDDDSDSQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDERSQDII
RARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA

Ligands and cofactors

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

Primary citation

Structural Insight into the Mechanism of sigma 32-Mediated Transcription Initiation of Bacterial RNA Polymerase. Lu, Q., Chen, T., Wang, J. et al. Biomolecules (2023) 13. DOI 10.3390/biom13050738 · 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…
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…
9YMV 2.6 Å, De novo initial transcribing RNA polymerase with pretranslocated 3-mer RNA / product…

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