8PEN: Fully recruited RfaH

Name: PDB 8PEN: fully recruited RfaH bound to E. coli transcription complex paused at ops site (alternative state of RfaH)
Published: 2024-04-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

fully recruited RfaH bound to E. coli transcription complex paused at ops site (alternative state of RfaH). Determined by electron microscopy at 3.1 Å resolution. Released 24 Apr 2024.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Escherichia coli
Chains: 9
Atoms: 27,734
Mol. weight: 439.45 kDa
Ligands: ZN, MG
Released: 24 Apr 2024

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

Secondary structure: helices and β-sheets

8PEN contains 146 α-helices and 214 β-strands across 6 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: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	64
β-strand	23-32	10	64
α-helix	35-47	13
β-strand	52-61	10	65
β-strand	74	1	66
α-helix	78-86	9
β-strand	90-91	2	67
β-strand	97-105	9	65
β-strand	108-111	4	66
α-helix	112-114	3
β-strand	115	1	65
β-strand	122-123	2	67
β-strand	129-133	5	66
β-strand	139-150	12	65
β-strand	152-153	2	68
α-helix	155-161	7
α-helix	165-167	3
β-strand	170-172	3	65
β-strand	175-176	2	68
β-strand	180-189	10	64
β-strand	198-207	10	64
α-helix	213-233	21

Chain H: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	15-20	6	69
β-strand	23-31	9	69
α-helix	35-49	15
β-strand	52-61	10	70
β-strand	74	1	71
α-helix	78-87	10
β-strand	90	1	72
β-strand	97-105	9	70
β-strand	108-111	4	71
α-helix	112-114	3
β-strand	115	1	70
β-strand	123	1	72
β-strand	129-133	5	71
β-strand	139-150	12	70
α-helix	155-159	5
β-strand	170-172	3	70
β-strand	181-190	10	69
β-strand	198-206	9	69
α-helix	213-227	15
α-helix	229-232	4

Chain I: 59 helices, 95 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
α-helix	11-12	2
β-strand	13-14	2	4
α-helix	19-20	2
α-helix	23-26	4
α-helix	29-39	11
α-helix	48-56	9
β-strand	59	1	5
β-strand	66-75	10	5
α-helix	76-78	3
α-helix	82-88	7
β-strand	93-105	13	5
β-strand	114-128	15	5
β-strand	130	1	6
β-strand	136-138	3	6
β-strand	141-145	5	6
β-strand	147	1	7
β-strand	148-151	4	8
α-helix	152	1
β-strand	154-160	7	9
β-strand	171-177	7	9
β-strand	180	1	10
β-strand	184-189	6	9
β-strand	193-198	6	9
β-strand	204-205	2	9
α-helix	207-212	6
α-helix	217-224	8
β-strand	227-231	5	11
β-strand	239-240	2	11
α-helix	243-246	4
β-strand	250	1	12
β-strand	256-257	2	13
β-strand	260-261	2	13
β-strand	268	1	12
α-helix	269-270	2
α-helix	271-280	10
β-strand	284-285	2	11
α-helix	289-294	6
β-strand	296-297	2	11
β-strand	301-303	3	14
β-strand	308-311	4	14
β-strand	315-316	2	11
α-helix	319-328	10
β-strand	332-336	5	11
α-helix	346-353	8
α-helix	359-370	12
α-helix	378-388	11
β-strand	396	1	10
α-helix	399-409	11
α-helix	422-437	16
α-helix	442-444	3
β-strand	451-454	4	8
α-helix	456-481	26
α-helix	489-492	4
α-helix	496-508	13
β-strand	512-514	3	6
α-helix	515-516	2
α-helix	520-527	8
β-strand	529-531	3	7
β-strand	533	1	15
β-strand	538	1	15
α-helix	545-548	4
α-helix	550-551	2
α-helix	552-554	3
β-strand	558	1	16
β-strand	572-574	3	7
β-strand	575	1	16
β-strand	576	1	17
β-strand	580-581	2	18
β-strand	587-595	9	18
β-strand	598-607	10	18
α-helix	608-613	6
β-strand	616-617	2	18
β-strand	623	1	19
α-helix	625-627	3
β-strand	629	1	19
β-strand	633-638	6	18
β-strand	641-646	6	18
β-strand	652-654	3	18
β-strand	662	1	17
α-helix	663-666	4
α-helix	676-686	11
β-strand	689	1	20
β-strand	700-701	2	4
α-helix	705-711	7
β-strand	716-717	2	21
β-strand	722-727	6	22
β-strand	731-736	6	22
α-helix	737	1
α-helix	741-742	2
β-strand	748-752	5	22
β-strand	757-758	2	23
β-strand	763	1	24
β-strand	764-765	2	23
β-strand	768-769	2	21
β-strand	776-777	2	22
β-strand	782-785	4	21
β-strand	789-790	2	25
β-strand	793-794	2	25
β-strand	798-804	7	26
β-strand	816-819	4	26
α-helix	820-825	6
β-strand	830-841	12	24
β-strand	849-850	2	27
α-helix	859-862	4
β-strand	865	1	28
β-strand	870	1	29
β-strand	871	1	28
α-helix	872	1
β-strand	876-877	2	24
β-strand	882	1	30
β-strand	884	1	29
β-strand	886-889	4	27
β-strand	913-915	3	27
β-strand	919	1	30
α-helix	920-921	2
β-strand	926-935	10	24
α-helix	940-942	3
α-helix	943-982	40
α-helix	986-991	6
α-helix	994-996	3
α-helix	1006-1037	32
β-strand	1046-1058	13	24
α-helix	1059-1060	2
β-strand	1065-1067	3	31
β-strand	1073-1075	3	31
β-strand	1076-1080	5	26
β-strand	1087	1	32
β-strand	1093	1	32
β-strand	1096-1098	3	26
α-helix	1102-1106	5
α-helix	1110-1133	24
α-helix	1138-1150	13
α-helix	1161-1163	3
α-helix	1168-1176	9
β-strand	1182-1183	2	4
α-helix	1192-1201	10
β-strand	1209-1210	2	26
β-strand	1213	1	32
β-strand	1220	1	32
β-strand	1225-1232	8	26
β-strand	1233-1234	2	31
β-strand	1235	1	20
α-helix	1239-1242	4
β-strand	1244-1246	3	33
β-strand	1251	1	34
β-strand	1258	1	34
β-strand	1269-1270	2	35
α-helix	1272-1280	9
α-helix	1285-1288	4
α-helix	1289-1296	8
α-helix	1298-1309	12
α-helix	1321-1332	12
β-strand	1335-1340	6	36

Chain J: 66 helices, 81 β-strands

Element	Residues	Length	Sheet
β-strand	19-24	6	36
α-helix	25-26	2
α-helix	27-33	7
β-strand	34-37	4	37
α-helix	51-52	2
α-helix	78-80	3
β-strand	84	1	38
β-strand	91	1	38
α-helix	95-99	5
β-strand	102-112	11	37
α-helix	115-118	4
α-helix	122	1
α-helix	123-127	5
α-helix	132-139	8
β-strand	144-148	5	39
β-strand	159-160	2	39
α-helix	162-171	10
β-strand	177-179	3	39
α-helix	182-190	9
α-helix	194-207	14
α-helix	211-229	19
α-helix	234-237	4
β-strand	238-244	7	37
α-helix	247-249	3
β-strand	253-254	2	40
β-strand	260-261	2	40
α-helix	264-284	21
α-helix	289-307	19
α-helix	315-316	2
β-strand	317	1	41
β-strand	323	1	41
α-helix	337	1
α-helix	338-342	5
β-strand	345-346	2	35
β-strand	350-354	5	33
β-strand	355-357	3	42
β-strand	365-369	5	43
α-helix	370-376	7
α-helix	378-388	11
α-helix	394-403	10
α-helix	406-415	10
β-strand	421-425	5	33
α-helix	431-433	3
β-strand	434-437	4	33
β-strand	438-442	5	43
β-strand	447-449	3	42
α-helix	454-457	4
β-strand	465-469	5	33
α-helix	474-482	9
β-strand	485	1	33
β-strand	491	1	44
β-strand	498	1	44
α-helix	505-513	9
β-strand	526-527	2	45
α-helix	530-538	9
β-strand	547-557	11	45
β-strand	563-573	11	45
α-helix	574-579	6
α-helix	589-591	3
α-helix	598-611	14
α-helix	615-635	21
α-helix	645-647	3
α-helix	650-669	20
α-helix	675-702	28
β-strand	705-709	5	46
β-strand	712-716	5	46
α-helix	721-727	7
α-helix	734-741	8
β-strand	745	1	47
β-strand	748	1	48
α-helix	753	1
β-strand	754	1	48
α-helix	755	1
β-strand	759	1	47
α-helix	769-803	35
β-strand	809-811	3	49
β-strand	820-822	3	50
β-strand	825-827	3	51
β-strand	828	1	52
β-strand	830-833	4	51
α-helix	835-839	5
β-strand	842-843	2	53
β-strand	844	1	50
α-helix	847	1
β-strand	848-849	2	54
α-helix	850	1
β-strand	856-858	3	54
β-strand	863-864	2	53
α-helix	866-873	8
β-strand	880-882	3	50
β-strand	894-895	2	49
α-helix	896-899	4
β-strand	901	1	55
β-strand	908	1	55
α-helix	909-910	2
α-helix	915-924	10
α-helix	925-927	3
β-strand	949-951	3	56
β-strand	956	1	57
β-strand	957-961	5	52
β-strand	965-967	3	56
β-strand	973-975	3	56
β-strand	981-985	5	52
β-strand	991-996	6	52
α-helix	997-998	2
β-strand	1002-1003	2	56
β-strand	1011	1	57
β-strand	1016-1019	4	56
β-strand	1024-1029	6	58
β-strand	1033-1036	4	59
β-strand	1042	1	58
β-strand	1046-1050	5	58
α-helix	1051	1
β-strand	1057-1061	5	58
α-helix	1062-1063	2
β-strand	1077-1081	5	59
β-strand	1087	1	59
α-helix	1088	1
β-strand	1089	1	60
α-helix	1090	1
β-strand	1096	1	60
β-strand	1098-1100	3	59
β-strand	1106-1107	2	58
β-strand	1113-1115	3	59
β-strand	1119-1125	7	58
α-helix	1138-1145	8
α-helix	1153-1155	3
β-strand	1156	1	61
β-strand	1161-1165	5	62
β-strand	1172-1178	7	62
β-strand	1186-1191	6	62
β-strand	1203-1204	2	62
β-strand	1209	1	61
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	63
β-strand	1279-1281	3	63
α-helix	1282-1295	14
β-strand	1301-1305	5	63
α-helix	1309-1314	6
α-helix	1319-1325	7
α-helix	1328-1338	11
β-strand	1341-1343	3	36
α-helix	1347-1353	7
α-helix	1361-1374	14

Chain K: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	7-13	7
α-helix	18-32	15
α-helix	35-37	3
α-helix	46-55	10
α-helix	61-83	23

Chain P: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	14-23	10
β-strand	27-29	3	1
β-strand	32-37	6	2
β-strand	44-49	6	2
β-strand	54-59	6	1
α-helix	66-70	5
β-strand	75-78	4	1
β-strand	80	1	3
β-strand	85	1	3
α-helix	86	1
α-helix	90-98	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription antitermination protein RfaH	P	protein	164	Escherichia coli	P0AFW0 (AlphaFold model)
DNA-directed RNA polymerase subunit beta	I	protein	1342	Escherichia coli	P0A8V2 (AlphaFold model)
DNA-directed RNA polymerase subunit beta'	J	protein	1416	Escherichia coli	P0A8T7 (AlphaFold model)
DNA-directed RNA polymerase subunit omega	K	protein	91	Escherichia coli	P0A800 (AlphaFold model)
DNA-directed RNA polymerase subunit alpha	G, H	protein	329	Escherichia coli	P0A7Z4
non-template DNA	A	DNA	40	Escherichia coli
template DNA	B	DNA	40	Escherichia coli
RNA	R	RNA	17	Escherichia coli

Sequence of entity 1 (P), FASTA

>8PEN_1 Transcription antitermination protein RfaH (chains P)
GHMQSWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVE
FDPEVIHTTTINATRGVSHFVRFGASPAIVPSAVIHQLSVYKPKDIVDPATPYPGDKVII
TEGAFEGFQAIFTEPDGEARSMLLLNLINKEIKHSVKNTEFRKL

Sequence of entity 2 (I), FASTA

>8PEN_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

>8PEN_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
APQVTAEDASASLAELLNAGLGGSDNELEVHHHHHH

Sequence of entity 4 (K), FASTA

>8PEN_4 DNA-directed RNA polymerase subunit omega (chains K)
MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLIN
NQILDVRERQEQQEQEAAELQAVTAIAEGRR

Sequence of entity 5 (G, H), FASTA

>8PEN_5 DNA-directed RNA polymerase subunit alpha (chains G, H)
MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE
IDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGD
VEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPV
ERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP
EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL
TEIKDVLASRGLSLGMRLENWPPASIADE

Sequence of entity 6 (A), FASTA

>8PEN_6 non-template DNA (chains A)
CACCACCACGCGGGCGGTAGCGTGCTTTTTTCGATCTTCC

Sequence of entity 7 (B), FASTA

>8PEN_7 template DNA (chains B)
GGAAGATCGAAAAAAGCACGCTACCGCCCGCGTGGTGGTG

Sequence of entity 8 (R), FASTA

>8PEN_8 RNA (chains R)
UUCUUUGGCGGUAGCGU

Ligands and cofactors

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

Primary citation

Concerted transformation of a hyper-paused transcription complex and its reinforcing protein. Zuber, P.K., Said, N., Hilal, T. et al. Nat Commun (2024) 15:3040-3040. DOI 10.1038/s41467-024-47368-4 · PubMed

Other PDB entries of the same protein (UniProt P0AFW0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2OUG 2.1 Å, Crystal structure of the RfaH transcription factor at 2.1A resolution
5OND 2.1 Å, RfaH from Escherichia coli in complex with ops DNA
8PIB 2.6 Å, autoinhibited RfaH bound to E. coli transcription complex paused at ops site (encounter…
8PID 3.0 Å, backtracked E. coli transcription complex paused at ops site and bound to RfaH
8PFG 3.1 Å, autoinhibited RfaH bound to E. coli transcription complex paused at ops site (encounter…
8PHK 3.1 Å, fully recruited RfaH bound to E. coli transcription complex paused at ops site
8URY 3.1 Å, Escherichia coli transcription-translation coupled complex class B (TTC-B) containing…
8PIL 3.2 Å, E. coli transcription complex paused at ops site and bound to RfaH and NusA
8UQL 3.2 Å, Escherichia coli transcription-translation coupled complex class B (TTC-B) containing…
8PFJ 3.4 Å, fully recruited RfaH bound to E. coli transcription complex paused at ops site (not…
8PIM 3.4 Å, fully recruited RfaH bound to E. coli transcription complex paused at ops site (not…
8UR0 3.4 Å, Escherichia coli transcription-translation coupled complex class B (TTC-B) containing…

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