8SY5: DNA-directed RNA polymerase subunit alpha

E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dS-BTP base pair in the active site. Determined by electron microscopy at 2.7 Å resolution. Released 27 Dec 2023.

Method: Electron microscopy
Resolution: 2.7 Å
Organisms: Escherichia coli, synthetic construct
Chains: 8
Atoms: 21,411
Mol. weight: 410.28 kDa
Ligands: ZN, MG, X0F
Released: 27 Dec 2023

Explore 8SY5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SY5 contains 139 α-helices and 150 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: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	13-20	8	1
β-strand	23-31	9	1
α-helix	35-49	15
β-strand	52-61	10	2
β-strand	74	1	3
α-helix	78-86	9
β-strand	90-92	3	4
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	4
β-strand	129-133	5	3
β-strand	139-150	12	2
β-strand	152-153	2	5
α-helix	155-157	3
β-strand	171-172	2	2
β-strand	175-176	2	5
β-strand	180-192	13	1
β-strand	195-207	13	1
α-helix	213-225	13
α-helix	226-228	3

Chain G: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	12-20	9	6
β-strand	23-31	9	6
α-helix	35-47	13
β-strand	53-61	9	7
β-strand	74	1	8
α-helix	78-85	8
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	121-123	3	9
β-strand	129-133	5	8
β-strand	139-149	11	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	192	1	11
β-strand	195	1	11
β-strand	199-207	9	6
α-helix	213-227	15
α-helix	228-231	4

Chain I: 55 helices, 67 β-strands

Element	Residues	Length	Sheet
α-helix	11-12	2
β-strand	13-14	2	12
α-helix	19-20	2
α-helix	29-39	11
α-helix	49-54	6
β-strand	69-75	7	13
α-helix	82-88	7
β-strand	93-101	9	13
β-strand	119-128	10	13
β-strand	136-137	2	14
β-strand	142-145	4	14
α-helix	146	1
β-strand	147-151	5	15
α-helix	152	1
β-strand	154-160	7	16
β-strand	171-177	7	16
β-strand	180	1	17
β-strand	184-187	4	16
β-strand	195-197	3	16
β-strand	204-205	2	16
α-helix	207-211	5
α-helix	217-224	8
α-helix	346-353	8
α-helix	359-370	12
α-helix	378-389	12
β-strand	396	1	17
α-helix	399-408	10
α-helix	422-437	16
α-helix	442-444	3
β-strand	451-454	4	15
α-helix	456-478	23
α-helix	489-492	4
α-helix	496-508	13
β-strand	512-514	3	14
α-helix	515-516	2
α-helix	520-527	8
β-strand	529-531	3	15
α-helix	550-551	2
α-helix	552-554	3
β-strand	558	1	18
β-strand	572-574	3	15
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	610-613	4
β-strand	616-617	2	19
β-strand	623	1	20
β-strand	628	1	19
β-strand	629	1	20
β-strand	634-638	5	19
β-strand	641-645	5	19
α-helix	647-649	3
β-strand	652-653	2	19
α-helix	665-667	3
α-helix	671-673	3
α-helix	676-685	10
β-strand	689	1	21
β-strand	700-701	2	12
α-helix	705-712	8
β-strand	716-717	2	22
β-strand	722-728	7	23
β-strand	731-736	6	23
α-helix	737	1
α-helix	738-740	3
β-strand	748-752	5	23
β-strand	757-758	2	24
β-strand	764-765	2	24
β-strand	768-769	2	22
β-strand	776-777	2	23
β-strand	782-785	4	22
β-strand	789-790	2	25
β-strand	793-794	2	25
β-strand	798-804	7	26
β-strand	815-819	5	26
α-helix	820-824	5
β-strand	830-841	12	27
α-helix	860-862	3
β-strand	865	1	28
β-strand	871	1	28
α-helix	872	1
β-strand	876-877	2	27
α-helix	920-921	2
β-strand	926-935	10	27
α-helix	943-944	2
α-helix	945-949	5
α-helix	950-975	26
α-helix	1018-1036	19
β-strand	1046-1058	13	27
β-strand	1065-1067	3	26
β-strand	1073-1080	8	26
α-helix	1082-1084	3
β-strand	1087	1	29
α-helix	1092	1
β-strand	1093	1	29
α-helix	1094	1
β-strand	1096-1098	3	26
α-helix	1100-1102	3
α-helix	1110-1133	24
α-helix	1138-1149	12
α-helix	1161-1163	3
α-helix	1166-1175	10
β-strand	1182-1183	2	12
α-helix	1192-1201	10
β-strand	1209-1210	2	26
β-strand	1213	1	29
α-helix	1219	1
β-strand	1220	1	29
α-helix	1221	1
β-strand	1225-1234	10	26
β-strand	1235	1	21
α-helix	1239-1241	3
β-strand	1244-1246	3	30
β-strand	1251	1	31
β-strand	1258	1	31
β-strand	1269-1270	2	32
α-helix	1272-1281	10
α-helix	1284-1288	5
α-helix	1289-1293	5
α-helix	1298-1310	13
α-helix	1321-1331	11
β-strand	1335-1340	6	33

Chain J: 64 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	19-24	6	33
α-helix	27-33	7
β-strand	34	1	34
α-helix	51-52	2
α-helix	59-62	4
α-helix	78-80	3
β-strand	84	1	35
β-strand	91	1	35
α-helix	95-99	5
β-strand	102	1	34
β-strand	103-112	10	36
α-helix	114-117	4
α-helix	132-139	8
α-helix	182-190	9
α-helix	194-204	11
α-helix	217-230	14
α-helix	234-237	4
β-strand	238-244	7	36
α-helix	247-249	3
β-strand	253-254	2	37
β-strand	260-261	2	37
α-helix	265-285	21
α-helix	289-307	19
β-strand	317	1	38
β-strand	323	1	38
α-helix	324-325	2
α-helix	327-330	4
α-helix	337	1
α-helix	338-342	5
β-strand	345-346	2	32
β-strand	350-354	5	30
β-strand	355-357	3	39
β-strand	365-369	5	39
α-helix	370-376	7
α-helix	378-387	10
α-helix	394-403	10
α-helix	408-414	7
β-strand	421-424	4	30
α-helix	431-433	3
β-strand	434-437	4	30
β-strand	438-442	5	39
β-strand	447-449	3	39
α-helix	451-453	3
α-helix	454-457	4
β-strand	465-469	5	30
α-helix	474-479	6
α-helix	480-484	5
β-strand	485	1	30
β-strand	491	1	40
β-strand	498	1	40
α-helix	505-514	10
β-strand	526-527	2	41
α-helix	530-539	10
β-strand	547-557	11	41
β-strand	563-573	11	41
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	650-663	14
α-helix	666-669	4
α-helix	678-702	25
β-strand	703	1	42
β-strand	707-709	3	43
β-strand	712-714	3	43
β-strand	717	1	42
α-helix	721-728	8
α-helix	734-741	8
β-strand	745	1	44
β-strand	748	1	45
α-helix	753	1
β-strand	754	1	45
α-helix	755	1
β-strand	759	1	44
α-helix	766-767	2
α-helix	769-774	6
α-helix	776-788	13
α-helix	790-803	14
β-strand	808	1	46
β-strand	809-811	3	47
β-strand	820-822	3	48
α-helix	836-839	4
β-strand	843	1	49
β-strand	844	1	48
β-strand	863	1	49
α-helix	866-874	9
β-strand	880-882	3	48
β-strand	894-895	2	47
α-helix	896-899	4
β-strand	901	1	50
β-strand	908	1	50
α-helix	909-910	2
β-strand	914	1	46
α-helix	915-931	17
α-helix	934-936	3
α-helix	1138-1144	7
α-helix	1217-1224	8
α-helix	1226-1243	18
α-helix	1251-1260	10
β-strand	1263-1265	3	51
β-strand	1279-1281	3	51
α-helix	1282-1294	13
β-strand	1303-1304	2	51
α-helix	1309-1314	6
α-helix	1319-1325	7
α-helix	1328-1338	11
β-strand	1341-1342	2	33
α-helix	1347-1353	7
α-helix	1360-1362	3
α-helix	1363-1371	9

Chain K: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	15-21	7
α-helix	24-36	13
α-helix	37-41	5
α-helix	54-64	11
α-helix	69-79	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA-directed RNA polymerase subunit alpha	A, G	protein	329	Escherichia coli	P0A7Z4 (AlphaFold model)
DNA-directed RNA polymerase subunit beta	I	protein	1342	Escherichia coli	P0A8V2 (AlphaFold model)
DNA-directed RNA polymerase subunit beta'	J	protein	1430	Escherichia coli	P0A8T7 (AlphaFold model)
DNA-directed RNA polymerase subunit omega	K	protein	91	Escherichia coli	P0A800 (AlphaFold model)
Non-template single stranded DNA	N	DNA	18	synthetic construct
RNA oligomer	R	RNA	9	synthetic construct
Template single stranded DNA	T	DNA	29	synthetic construct

Sequence of entity 1 (A, G), FASTA

>8SY5_1 DNA-directed RNA polymerase subunit alpha (chains A, G)
MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE
IDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGD
VEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPV
ERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP
EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL
TEIKDVLASRGLSLGMRLENWPPASIADE

Sequence of entity 2 (I), FASTA

>8SY5_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

>8SY5_3 DNA-directed RNA polymerase subunit beta' (chains J)
MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCAR
IFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSL
PSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDEFDAKM
GAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILT
VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQ
EAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPY
LRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHP
VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA
RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSG
LASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKA
ISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAE
VAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFN
SIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGAR
KGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVL
GRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYG
RDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKL
SNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANW
DPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKI
VDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDITGGLPR
VADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFE
GERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQM
LRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFI
SAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAGEAPA
APQVTAEDASASLAELLNAGLGGSDNELELEVLFQGPSSGHHHHHHHHHH

Sequence of entity 4 (K), FASTA

>8SY5_4 DNA-directed RNA polymerase subunit omega (chains K)
MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLIN
NQILDVRERQEQQEQEAAELQAVTAIAEGRR

Sequence of entity 5 (N), FASTA

>8SY5_5 Non-template single stranded DNA (chains N)
TCAGCGAGAGAGAGAAGG

Sequence of entity 6 (R), FASTA

>8SY5_6 RNA oligomer (chains R)
AUCGAGAGG

Sequence of entity 7 (T), FASTA

>8SY5_7 Template single stranded DNA (chains T)
CCTTCTCTCTCTCGCTGAXCCTCTCGATG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	1
X0F	2-oxo-2-hydroadenosine 5'-(tetrahydrogen triphosphate)	C10 H16 N5 O14 P3	1

Primary citation

A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase. Oh, J., Shan, Z., Hoshika, S. et al. Nat Commun (2023) 14:8219-8219. DOI 10.1038/s41467-023-43735-9 · 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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