9YMU: DNA-directed RNA polymerase subunit beta

De novo initial transcribing RNA polymerase with 2-mer RNA and bound CTP / Michaelis complex (RPitc2+CTP). Determined by electron microscopy at 2.7 Å resolution. Released 29 Apr 2026.

Method
Electron microscopy
Resolution
2.7 Å
Organisms
Escherichia coli, Escherichia phage T7
Chains
9
Atoms
32,296
Mol. weight
522.33 kDa
Ligands
MG, ZN, CTP
Released
29 Apr 2026

Explore 9YMU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9YMU contains 177 α-helices and 213 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: 8 helices, 16 β-strands

ElementResiduesLengthSheet
α-helix9-113
β-strand12-18760
β-strand23-31960
α-helix35-4713
β-strand52-611061
β-strand74162
α-helix78-858
β-strand90-92363
β-strand97-105961
β-strand108-111462
α-helix112-1143
β-strand115161
α-helix116-1172
β-strand121-123363
β-strand129-133562
β-strand139-1501261
β-strand152-153264
α-helix155-1573
β-strand170-172361
β-strand175-176264
β-strand180-1891060
β-strand199-207960
α-helix213-22715
α-helix229-2324
Chain H: 5 helices, 17 β-strands
ElementResiduesLengthSheet
β-strand13-18665
β-strand23-31965
α-helix35-4915
β-strand52-60966
β-strand61167
β-strand64167
α-helix78-869
β-strand90-92368
β-strand97-105966
β-strand108-111469
α-helix112-1143
β-strand115166
α-helix116-1172
β-strand121-123368
β-strand129-133569
β-strand139-1501266
β-strand152-153270
β-strand170-172366
β-strand175-176270
β-strand180-1921365
β-strand195-2071365
α-helix213-22614
Chain I: 58 helices, 96 β-strands
ElementResiduesLengthSheet
α-helix5-84
α-helix11-122
β-strand13-1421
α-helix29-3911
α-helix49-568
α-helix57-582
β-strand59-6022
β-strand66-75102
α-helix82-887
β-strand93-105132
β-strand114-128152
β-strand13013
β-strand136-13833
β-strand141-14553
β-strand147-15154
α-helix1521
β-strand154-15855
β-strand173-17755
β-strand18016
β-strand184-18745
β-strand195-19845
β-strand204-20525
α-helix207-2126
α-helix217-2248
β-strand227-23377
β-strand236-24057
α-helix243-2464
β-strand25018
β-strand255-25739
β-strand260-26349
β-strand26818
α-helix271-28010
β-strand284-28747
α-helix289-2924
β-strand296110
β-strand29717
β-strand301-303311
β-strand308-311411
β-strand316110
α-helix319-3268
β-strand332-33657
α-helix346-3538
α-helix359-37012
α-helix378-38912
β-strand39616
α-helix398-40811
α-helix422-43716
α-helix442-4443
β-strand451-45444
α-helix456-48025
α-helix489-4924
α-helix496-50813
β-strand512-51433
α-helix515-5162
α-helix520-5278
β-strand529-53134
α-helix540-5423
α-helix552-5543
β-strand558112
β-strand572-57434
β-strand575112
β-strand576113
β-strand580-581214
β-strand587-595914
β-strand598-6071014
α-helix608-6114
β-strand616-617214
β-strand623115
β-strand629115
β-strand633-637514
β-strand642-646514
β-strand652-653214
β-strand662113
α-helix665-6673
α-helix671-6733
β-strand674116
α-helix676-68611
β-strand689117
α-helix690-6912
β-strand700-70121
α-helix705-7128
β-strand716-717218
β-strand722-727619
β-strand731-736619
β-strand748-752519
β-strand757-758220
β-strand764-765220
β-strand768-769218
β-strand776-777219
β-strand782-785418
β-strand789-790221
β-strand793-794221
β-strand798-804722
β-strand815-819522
α-helix820-8245
β-strand830-8411223
β-strand842124
β-strand847124
β-strand849125
α-helix860-8623
β-strand865126
β-strand870127
β-strand871126
α-helix8721
β-strand876-877223
β-strand882-884327
β-strand887-889325
α-helix897-90610
α-helix909-9113
β-strand913-915325
β-strand918-919227
α-helix920-9212
β-strand926-9351023
α-helix943-98038
α-helix988-9914
α-helix994-9985
α-helix1006-10094
α-helix1011-103727
α-helix1042-10432
β-strand1046-10581323
β-strand1065-1067322
β-strand1073-1080822
α-helix1082-10843
β-strand1087128
β-strand1093128
β-strand1096-1098322
α-helix1102-11065
β-strand1108116
α-helix1110-113324
α-helix1138-115013
α-helix1161-11633
α-helix1168-11769
β-strand1182-118321
α-helix1192-120110
β-strand1209-1210222
β-strand1213128
α-helix12191
β-strand1220128
α-helix12211
β-strand1225-12341022
β-strand1235117
α-helix1239-12413
β-strand1244-1246329
β-strand1251130
β-strand1252131
β-strand1258130
β-strand1260132
β-strand1267132
β-strand1268-1270333
α-helix1272-12809
α-helix1284-12918
α-helix1298-130912
α-helix1321-133212
β-strand1335-1340634
Chain J: 72 helices, 80 β-strands
ElementResiduesLengthSheet
β-strand19-24634
α-helix27-337
β-strand34-37435
β-strand44136
α-helix501
β-strand51136
α-helix521
α-helix59-624
α-helix78-803
β-strand84137
β-strand91137
α-helix95-995
β-strand102-1121135
α-helix115-1184
α-helix1221
α-helix123-1286
α-helix132-1398
β-strand144-148538
α-helix154-1552
β-strand159-160238
α-helix162-17211
β-strand177-179338
α-helix181-19010
α-helix194-20613
α-helix211-22919
α-helix234-2374
β-strand238-244735
α-helix247-2493
β-strand252-254339
β-strand260-262339
α-helix265-28521
α-helix289-30719
α-helix315-3162
β-strand317140
β-strand323140
α-helix324-3252
α-helix327-3315
α-helix3371
α-helix338-3425
β-strand345-347333
β-strand350-354529
β-strand355-357341
β-strand365-369541
α-helix370-3767
α-helix378-38811
α-helix394-40310
α-helix406-41510
β-strand421-424429
α-helix431-4333
β-strand434-437429
β-strand438-442541
β-strand447-449341
α-helix454-4574
β-strand465-469529
α-helix474-4829
β-strand485129
α-helix486-4883
β-strand491142
β-strand498142
α-helix505-5139
β-strand526-527243
α-helix530-5389
β-strand547-5571143
β-strand563-5731143
α-helix574-5796
α-helix580-5823
α-helix5841
α-helix589-5913
α-helix598-61114
α-helix614-63522
α-helix645-6473
α-helix649-66921
α-helix675-70127
β-strand703-707544
β-strand713-717544
α-helix721-7288
α-helix734-7418
β-strand745-748445
α-helix7531
β-strand754-759645
α-helix769-78820
α-helix790-80415
β-strand809-811346
β-strand820-822347
β-strand825-827348
β-strand828149
β-strand830-833448
α-helix835-8395
β-strand843150
β-strand844147
β-strand848-849251
β-strand856-858351
β-strand863150
α-helix866-8749
β-strand880-882347
β-strand894-895246
α-helix896-8994
β-strand901152
β-strand908152
α-helix909-9102
α-helix915-93117
β-strand940145
α-helix945-9473
β-strand949-952453
β-strand956-961649
β-strand965-967353
β-strand973-975353
β-strand980-985649
β-strand991-997749
β-strand1002-1003253
β-strand1010-1011249
β-strand1015-1019553
β-strand1024-1028554
β-strand1033-1038655
β-strand1046-1050554
β-strand1057-1061554
α-helix10621
α-helix1070-10723
β-strand1077-1081555
β-strand1087155
α-helix10881
β-strand1089156
α-helix10901
β-strand1096156
β-strand1100155
β-strand1106-1107254
β-strand1114-1115255
β-strand1120-1125654
α-helix1134-114512
α-helix1153-11542
β-strand1155-1156257
β-strand1161-1165558
β-strand1172-1178758
β-strand1186-1191658
α-helix1195-11962
β-strand1203-1204258
β-strand1209-1211357
α-helix1214-12163
α-helix1217-12237
α-helix1226-124318
α-helix1250-125910
β-strand1263-1268659
β-strand1279-1281359
α-helix1282-129413
β-strand1301-1305559
α-helix1309-13146
α-helix1319-13257
α-helix1328-133811
β-strand1341-1342234
α-helix1347-13526
α-helix1360-13623
α-helix1363-137412
Chain K: 5 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix7-137
α-helix16-3116
α-helix35-373
α-helix46-5611
α-helix61-7717
Chain L: 29 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix97-1059
α-helix113-13321
α-helix138-15215
α-helix215-23319
α-helix245-25814
α-helix263-29533
α-helix299-3068
α-helix314-3196
α-helix325-3295
α-helix330-3323
α-helix334-35118
α-helix355-38228
α-helix384-3929
α-helix401-41717
α-helix421-4233
α-helix427-44620
α-helix454-47421
α-helix477-4793
α-helix480-4878
α-helix491-4977
α-helix503-5042
β-strand505-506239
β-strand510171
β-strand518171
α-helix519-5224
α-helix5231
β-strand524131
α-helix5251
α-helix531-54818
α-helix553-56311
α-helix573-5797
α-helix584-59815
α-helix605-6106

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA-directed RNA polymerase subunit betaIprotein1342Escherichia coliP0A8V2 (AlphaFold model)
DNA-directed RNA polymerase subunit beta'Jprotein1415Escherichia coliP0A8T7 (AlphaFold model)
DNA-directed RNA polymerase subunit omegaKprotein91Escherichia coliP0A800 (AlphaFold model)
T7A1 promoter fragment non-template strandPDNA97Escherichia phage T7
Nascent RNARRNA2Escherichia coli
DNA-directed RNA polymerase subunit alphaG, Hprotein329Escherichia coliP0A7Z4 (AlphaFold model)
RNA polymerase sigma factor RpoDLprotein616Escherichia coliP00579
T7A1 promoter fragment template strandQDNA97Escherichia phage T7
Sequence of entity 1 (I), FASTA
>9YMU_1 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 2 (J), FASTA
>9YMU_2 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
APQVTAEDASASLAELLNAGLGGSDNELELEVLFQ
Sequence of entity 3 (K), FASTA
>9YMU_3 DNA-directed RNA polymerase subunit omega (chains K)
MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLIN
NQILDVRERQEQQEQEAAELQAVTAIAEGRR
Sequence of entity 4 (P), FASTA
>9YMU_4 T7A1 promoter fragment non-template strand (chains P)
GCTTAATTTAAAATTTATCAAAAAGAGTATTGACTTAAAGTCTAACCTATAGGATACTTA
CAGCCATCGAGAGGGACACGGCGAATAGCCATCCCGG
Sequence of entity 5 (R), FASTA
>9YMU_5 Nascent RNA (chains R)
AU
Sequence of entity 6 (G, H), FASTA
>9YMU_6 DNA-directed RNA polymerase subunit alpha (chains G, H)
MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE
IDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGD
VEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPV
ERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP
EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL
TEIKDVLASRGLSLGMRLENWPPASIADE
Sequence of entity 7 (L), FASTA
>9YMU_7 RNA polymerase sigma factor RpoD (chains L)
SEFMEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVME
EAPDADDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEI
DIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPT
ATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKA
KGRSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKM
PKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQ
VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD
KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE
PTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATT
ESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRK
LRHPSRSEVLRSFLDD
Sequence of entity 8 (Q), FASTA
>9YMU_8 T7A1 promoter fragment template strand (chains Q)
CCGGGATGGCTATTCGCCGTGTCCCTCTCGATGGCTGTAAGTATCCTATAGGTTAGACTT
TAAGTCAATACTCTTTTTGATAAATTTTAAATTAAGC

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg2
ZNZinc ionZn2
CTPCytidine-5'-triphosphateC9 H16 N3 O14 P31

Primary citation

Structural basis for multi-subunit DNA-dependent RNA polymerase catalytic activity. Mueller, A.U., Darst, S.A. Mol Cell (2026) 86:1881. DOI 10.1016/j.molcel.2026.03.033 · PubMed

Other PDB entries of the same protein (UniProt P0A8V2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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