8FVW: E.coli transcription elongation complex

CryoEM structure of E.coli transcription elongation complex bound to ppGpp. Determined by electron microscopy at 2.1 Å resolution. Released 5 Apr 2023.

Method: Electron microscopy
Resolution: 2.1 Å
Organisms: Escherichia coli K-12, Escherichia coli
Chains: 8
Atoms: 26,108
Mol. weight: 429.2 kDa
Ligands: G4P, MG, ZN
Released: 5 Apr 2023

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

Secondary structure: helices and β-sheets

8FVW contains 162 α-helices and 205 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 D: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
β-strand	12-18	7	1
β-strand	23-31	9	1
α-helix	35-50	16
β-strand	52-61	10	2
β-strand	74	1	3
α-helix	78-86	9
β-strand	90-92	3	2
β-strand	97-105	9	2
β-strand	108-111	4	3
α-helix	112-114	3
β-strand	115	1	2
α-helix	116-117	2
β-strand	121-123	3	2
β-strand	129-133	5	3
β-strand	139-150	12	2
β-strand	152-153	2	4
β-strand	170-172	3	2
β-strand	175-176	2	4
β-strand	180-189	10	1
β-strand	199-207	9	1
α-helix	213-232	20

Chain E: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	5
β-strand	23-31	9	5
α-helix	35-49	15
β-strand	52-61	10	6
β-strand	74	1	7
α-helix	78-86	9
β-strand	90-92	3	8
β-strand	97-105	9	6
β-strand	108-111	4	7
α-helix	112-114	3
β-strand	115	1	6
α-helix	116-117	2
β-strand	121-123	3	8
β-strand	129-133	5	7
β-strand	139-150	12	6
β-strand	152-153	2	9
α-helix	155-157	3
β-strand	171-172	2	6
β-strand	175-176	2	9
β-strand	180-190	11	5
β-strand	198-207	10	5
α-helix	213-227	15

Chain F: 67 helices, 96 β-strands

Element	Residues	Length	Sheet
α-helix	11-12	2
β-strand	13-14	2	10
α-helix	23-25	3
α-helix	29-39	11
α-helix	48-54	7
β-strand	59-60	2	11
β-strand	66-75	10	11
α-helix	76-78	3
α-helix	82-88	7
β-strand	93-105	13	11
α-helix	106	1
β-strand	114-128	15	11
α-helix	129	1
β-strand	130	1	12
β-strand	136-138	3	12
β-strand	141-145	5	12
β-strand	147-151	5	13
α-helix	152	1
β-strand	154-160	7	14
α-helix	170	1
β-strand	171-177	7	14
β-strand	180	1	15
β-strand	184-188	5	14
β-strand	194-198	5	14
β-strand	204-205	2	14
α-helix	207-212	6
α-helix	217-224	8
α-helix	226	1
β-strand	227-231	5	16
β-strand	239-240	2	16
α-helix	243-246	4
β-strand	250	1	17
β-strand	255-257	3	18
β-strand	260-263	4	18
β-strand	268	1	17
α-helix	271-276	6
β-strand	284-285	2	16
α-helix	290-294	5
β-strand	296-297	2	16
β-strand	301	1	19
β-strand	311	1	19
β-strand	315-316	2	16
α-helix	319-327	9
β-strand	332-336	5	16
α-helix	346-353	8
α-helix	359-370	12
α-helix	378-389	12
β-strand	396	1	15
α-helix	399-408	10
α-helix	422-436	15
α-helix	442-444	3
β-strand	451-454	4	13
α-helix	456-481	26
α-helix	489-492	4
α-helix	496-508	13
β-strand	512-514	3	12
α-helix	520-528	9
β-strand	529-531	3	13
α-helix	545-548	4
α-helix	552-554	3
β-strand	558	1	20
β-strand	572-574	3	13
β-strand	575	1	20
β-strand	576	1	21
β-strand	580-581	2	22
β-strand	587-595	9	22
β-strand	598-607	10	22
α-helix	608-611	4
β-strand	616-617	2	22
β-strand	623	1	23
β-strand	628	1	22
β-strand	629	1	23
β-strand	634-637	4	22
β-strand	642-645	4	22
β-strand	652-654	3	22
β-strand	662	1	21
α-helix	663-666	4
α-helix	671-673	3
β-strand	674	1	24
α-helix	676-686	11
β-strand	689	1	25
α-helix	690-691	2
β-strand	700-701	2	10
α-helix	705-712	8
β-strand	716-717	2	26
β-strand	722-728	7	27
β-strand	731-736	6	27
α-helix	738-740	3
β-strand	748-752	5	27
α-helix	753-754	2
β-strand	757-758	2	28
β-strand	763	1	29
β-strand	764-765	2	28
β-strand	768-769	2	26
β-strand	776-777	2	27
β-strand	782-785	4	26
β-strand	789-790	2	30
β-strand	793-794	2	30
β-strand	798-804	7	31
α-helix	812-814	3
β-strand	816-819	4	31
α-helix	820-824	5
β-strand	830-841	12	29
β-strand	842	1	32
β-strand	847	1	32
β-strand	849-850	2	33
α-helix	860-862	3
β-strand	865	1	34
β-strand	870	1	35
β-strand	871	1	34
α-helix	872	1
β-strand	876-877	2	29
β-strand	882-884	3	35
β-strand	886-888	3	33
β-strand	914-915	2	33
β-strand	918-919	2	35
α-helix	920-921	2
β-strand	926-935	10	29
α-helix	943-959	17
α-helix	962-979	18
α-helix	987-990	4
α-helix	1006-1009	4
α-helix	1011-1021	11
α-helix	1029-1037	9
β-strand	1046-1058	13	29
β-strand	1065-1067	3	36
β-strand	1073-1075	3	36
β-strand	1076-1080	5	31
α-helix	1082-1084	3
β-strand	1087	1	37
α-helix	1092	1
β-strand	1093	1	37
α-helix	1094	1
β-strand	1096-1098	3	31
α-helix	1100-1102	3
β-strand	1108	1	24
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	10
α-helix	1192-1201	10
β-strand	1209-1210	2	31
β-strand	1213	1	37
α-helix	1219	1
β-strand	1220	1	37
α-helix	1221	1
β-strand	1225-1232	8	31
β-strand	1233-1234	2	36
β-strand	1235	1	25
α-helix	1239-1242	4
β-strand	1244-1246	3	38
β-strand	1251	1	39
β-strand	1258	1	39
α-helix	1259	1
α-helix	1266-1268	3
β-strand	1269-1270	2	40
α-helix	1272-1281	10
α-helix	1284-1291	8
α-helix	1292-1296	5
α-helix	1298-1310	13
α-helix	1321-1332	12
β-strand	1335-1339	5	41

Chain G: 78 helices, 77 β-strands

Element	Residues	Length	Sheet
β-strand	19-24	6	41
α-helix	25-26	2
α-helix	27-33	7
β-strand	34-37	4	42
β-strand	44	1	43
α-helix	50	1
β-strand	51	1	43
α-helix	52	1
α-helix	59-62	4
β-strand	66	1	44
β-strand	69	1	44
β-strand	84	1	45
α-helix	90	1
β-strand	91	1	45
α-helix	92	1
α-helix	95-99	5
β-strand	102-112	11	42
α-helix	123-128	6
α-helix	132-139	8
β-strand	144-147	4	46
β-strand	159-160	2	46
α-helix	162-171	10
β-strand	177-179	3	46
α-helix	182-190	9
α-helix	194-204	11
α-helix	211-229	19
α-helix	234-237	4
β-strand	238-244	7	42
α-helix	247-249	3
β-strand	254-255	2	47
β-strand	259-260	2	47
α-helix	266-283	18
α-helix	289-307	19
β-strand	317	1	48
β-strand	323	1	48
α-helix	324-325	2
α-helix	327-331	5
α-helix	337	1
α-helix	338-342	5
β-strand	345-346	2	40
β-strand	350-354	5	38
β-strand	355-357	3	49
β-strand	365-369	5	49
α-helix	370-376	7
α-helix	378-387	10
α-helix	394-403	10
α-helix	406-415	10
β-strand	421-424	4	38
α-helix	431-433	3
β-strand	434-437	4	38
β-strand	438-442	5	49
β-strand	447-449	3	49
α-helix	451-453	3
α-helix	454-457	4
β-strand	465-469	5	38
α-helix	474-479	6
α-helix	480-484	5
β-strand	485	1	38
α-helix	486-488	3
β-strand	491	1	50
β-strand	498	1	50
α-helix	505-514	10
β-strand	526-527	2	51
α-helix	530-538	9
β-strand	547-557	11	51
β-strand	563-573	11	51
α-helix	574-580	7
α-helix	584	1
α-helix	589-591	3
α-helix	598-612	15
α-helix	614-635	22
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	52
β-strand	713-717	5	52
α-helix	721-728	8
α-helix	734-737	4
α-helix	738-742	5
β-strand	745	1	53
β-strand	748	1	54
α-helix	753	1
β-strand	754	1	54
α-helix	755	1
β-strand	759	1	53
α-helix	769-804	36
β-strand	809-811	3	55
β-strand	820-822	3	56
β-strand	825-826	2	57
β-strand	831-833	3	57
α-helix	835-839	5
β-strand	843	1	58
β-strand	844	1	56
α-helix	847	1
β-strand	848-849	2	59
α-helix	850	1
β-strand	856-858	3	59
β-strand	863	1	58
α-helix	866-874	9
β-strand	880-882	3	56
β-strand	894-895	2	55
α-helix	896-899	4
β-strand	901	1	60
β-strand	908	1	60
α-helix	909-910	2
α-helix	915-924	10
α-helix	925-929	5
β-strand	949-952	4	61
β-strand	956	1	62
β-strand	957-961	5	63
α-helix	972-974	3
β-strand	980-985	6	63
β-strand	991-997	7	63
β-strand	1002-1003	2	61
β-strand	1011	1	62
β-strand	1015-1019	5	61
β-strand	1034-1037	4	64
β-strand	1042	1	65
β-strand	1046-1049	4	65
β-strand	1058-1061	4	65
α-helix	1062-1063	2
α-helix	1069-1072	4
β-strand	1078-1081	4	64
β-strand	1098-1099	2	64
β-strand	1105-1107	3	65
β-strand	1114	1	64
α-helix	1138-1145	8
α-helix	1148-1150	3
α-helix	1153-1155	3
β-strand	1156	1	66
β-strand	1161-1167	7	67
β-strand	1174-1178	5	67
β-strand	1186-1189	4	67
β-strand	1203-1204	2	67
α-helix	1205	1
β-strand	1209	1	66
α-helix	1214-1216	3
α-helix	1217-1224	8
α-helix	1226-1243	18
α-helix	1250-1260	11
β-strand	1263-1268	6	68
α-helix	1275	1
β-strand	1279-1281	3	68
α-helix	1282-1295	14
α-helix	1298-1300	3
β-strand	1301-1305	5	68
α-helix	1309-1314	6
α-helix	1319-1325	7
α-helix	1328-1338	11
β-strand	1341-1343	3	41
α-helix	1347-1352	6
α-helix	1355-1357	3
α-helix	1360-1362	3
α-helix	1363-1371	9

Chain H: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	7-13	7
α-helix	16-31	16
α-helix	35-37	3
α-helix	46-55	10
α-helix	61-73	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA-directed RNA polymerase subunit alpha	D, E	protein	329	Escherichia coli K-12	P0A7Z4 (AlphaFold model)
DNA-directed RNA polymerase subunit beta	F	protein	1342	Escherichia coli K-12	P0A8V2 (AlphaFold model)
DNA-directed RNA polymerase subunit beta'	G	protein	1416	Escherichia coli K-12	P0A8T7 (AlphaFold model)
DNA-directed RNA polymerase subunit omega	H	protein	91	Escherichia coli K-12	P0A800 (AlphaFold model)
DNA (53-mer)	A	DNA	53	Escherichia coli
RNA (16-mer)	C	RNA	16	Escherichia coli
DNA (53-mer)	B	DNA	53	Escherichia coli

Sequence of entity 1 (D, E), FASTA

>8FVW_1 DNA-directed RNA polymerase subunit alpha (chains D, E)
MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE
IDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGD
VEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPV
ERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP
EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL
TEIKDVLASRGLSLGMRLENWPPASIADE

Sequence of entity 2 (F), FASTA

>8FVW_2 DNA-directed RNA polymerase subunit beta (chains F)
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 (G), FASTA

>8FVW_3 DNA-directed RNA polymerase subunit beta' (chains G)
VKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCAR
IFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSL
PSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDEFDAKM
GAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILT
VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQ
EAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPY
LRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHP
VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA
RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSG
LASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKA
ISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAE
VAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFN
SIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGAR
KGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVL
GRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYG
RDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKL
SNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANW
DPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKI
VDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDITGGLPR
VADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFE
GERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQM
LRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFI
SAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAGEAPA
APQVTAEDASASLAELLNAGLGGSDNELEVHHHHHH

Sequence of entity 4 (H), FASTA

>8FVW_4 DNA-directed RNA polymerase subunit omega (chains H)
MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLIN
NQILDVRERQEQQEQEAAELQAVTAIAEGRR

Sequence of entity 5 (A), FASTA

>8FVW_5 DNA (53-MER) (chains A)
CTTTGCTTAAGCATCCATATGGTTGGGCTACCTCTCCATGACGGCGAATACCC

Sequence of entity 6 (C), FASTA

>8FVW_6 RNA (16-MER) (chains C)
UCAAAGCGGAGAGGUA

Sequence of entity 7 (B), FASTA

>8FVW_7 DNA (53-MER) (chains B)
GGGTATTCGCCGTGTACCTCTCCTAGCCCAACCATATGGATGCTTAAGCAAAG

Ligands and cofactors

ID	Name	Formula	Copies
G4P	Guanosine-5',3'-tetraphosphate	C10 H17 N5 O17 P4	1
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	2

Water and common crystallization additives (NA) are not listed.

Primary citation

Control of transcription elongation and DNA repair by alarmone ppGpp. Weaver, J.W., Proshkin, S., Duan, W. et al. Nat Struct Mol Biol (2023) 30:600-607. DOI 10.1038/s41594-023-00948-2 · 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
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…
9YMV 2.6 Å, De novo initial transcribing RNA polymerase with pretranslocated 3-mer RNA / product…

Browse structure collections

About this viewer

MolViewer shows 8FVW 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.