9YMW: DNA-directed RNA polymerase subunit beta

De novo initial transcribing RNA polymerase with 5-mer RNA CCAUC (RPitc5a). 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
32,434
Mol. weight
522.91 kDa
Ligands
MG, ZN, POP
Released
29 Apr 2026

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

Secondary structure: helices and β-sheets

9YMW contains 189 α-helices and 216 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: 7 helices, 16 β-strands

ElementResiduesLengthSheet
α-helix8-114
β-strand12-20935
β-strand23-31935
α-helix35-5016
β-strand52-611036
β-strand74137
α-helix78-869
β-strand90-92338
β-strand97-105936
β-strand108-111437
α-helix112-1143
β-strand115136
α-helix116-1172
β-strand121-123338
β-strand129-133537
β-strand139-1501236
β-strand152-153239
β-strand170-172336
β-strand175-176239
β-strand180-1891035
β-strand199-207935
α-helix213-22715
α-helix229-2324
Chain H: 7 helices, 17 β-strands
ElementResiduesLengthSheet
α-helix9-113
β-strand13-20840
β-strand23-31940
α-helix35-4915
β-strand52-60941
β-strand61142
β-strand64142
β-strand74143
α-helix78-869
β-strand90-92344
β-strand97-105941
β-strand108-111443
α-helix112-1143
α-helix116-1172
β-strand121-123344
β-strand129-133543
β-strand139-1501241
β-strand152-153245
α-helix155-1573
β-strand171-172241
β-strand175-176245
β-strand180-1921340
β-strand195-2071340
α-helix213-22715
Chain I: 67 helices, 97 β-strands
ElementResiduesLengthSheet
α-helix11-122
β-strand13-1421
α-helix19-202
α-helix23-264
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
α-helix1461
β-strand147-15154
α-helix1521
β-strand154-15855
β-strand173-17755
β-strand18016
β-strand184-18855
β-strand194-19855
β-strand204-20525
α-helix207-2126
α-helix217-2248
β-strand227-23157
β-strand239-24027
α-helix243-2464
β-strand25018
β-strand255-25739
β-strand260-26349
α-helix2671
β-strand26818
α-helix2691
α-helix271-28010
β-strand284-28527
α-helix289-2924
β-strand296110
β-strand29717
β-strand301-302211
β-strand309-311311
β-strand316110
α-helix319-3268
β-strand332-33657
β-strand339112
β-strand343112
α-helix346-3538
α-helix359-37012
α-helix378-38912
β-strand39616
α-helix398-40811
α-helix422-43716
β-strand451-45444
α-helix456-48126
α-helix489-4924
α-helix496-50813
β-strand512-51433
α-helix515-5162
α-helix520-5278
β-strand529-53134
α-helix540-5423
α-helix546-5483
α-helix552-5543
β-strand558113
β-strand572-57434
β-strand575113
β-strand580-581214
β-strand587-595914
β-strand598-6071014
α-helix608-6114
β-strand616-617214
β-strand623115
β-strand628114
β-strand629115
β-strand633-637514
β-strand642-646514
α-helix647-6493
β-strand652-654314
α-helix665-6673
α-helix671-6733
β-strand674116
α-helix676-68510
α-helix686-6883
β-strand689117
α-helix690-6912
β-strand696118
β-strand700-70121
α-helix705-7128
β-strand716-717219
β-strand722-727620
β-strand731-736620
α-helix738-7403
α-helix741-7422
β-strand748-752520
β-strand757-758221
β-strand764-765221
β-strand768-769219
β-strand776-777220
β-strand782-785419
β-strand789-790222
β-strand793-794222
β-strand797118
β-strand798-804723
β-strand815-819523
α-helix820-8245
β-strand830-8411224
β-strand842125
β-strand847125
β-strand849126
β-strand865127
β-strand870128
β-strand871127
α-helix8721
β-strand876-877224
β-strand882-884328
β-strand887-889326
α-helix897-90610
β-strand913-915326
β-strand918-919228
α-helix920-9212
β-strand926-9351024
α-helix940-9412
α-helix943-96018
α-helix964-97815
α-helix986-9883
α-helix994-9996
α-helix1006-103429
α-helix1038-10403
α-helix1042-10432
β-strand1046-10581324
β-strand1065-1067323
β-strand1073-1080823
β-strand1087129
α-helix10921
β-strand1093129
α-helix10941
β-strand1096-1098323
α-helix1100-11023
β-strand1108116
α-helix1110-113324
α-helix1138-115013
α-helix1166-117510
β-strand1182-118321
α-helix1192-120110
β-strand1209-1210223
β-strand1213129
α-helix12191
β-strand1220129
α-helix12211
β-strand1225-12341023
β-strand1235117
α-helix1239-12413
β-strand1244-1246330
β-strand1251131
β-strand1252132
β-strand1258131
α-helix12671
β-strand1268-1270333
α-helix1272-12809
α-helix1284-12918
α-helix1298-131013
α-helix1321-133212
β-strand1335-1340634
Chain J: 74 helices, 82 β-strands
ElementResiduesLengthSheet
β-strand19-24634
α-helix27-337
β-strand34-37446
β-strand44147
α-helix501
β-strand51147
α-helix521
α-helix59-624
α-helix78-803
α-helix831
β-strand84148
α-helix851
β-strand91148
α-helix95-995
β-strand102-1121146
α-helix115-1184
α-helix1221
α-helix123-1286
α-helix132-1398
β-strand144-148549
α-helix154-1552
β-strand159-160249
α-helix162-17211
β-strand177-179349
α-helix182-1909
α-helix194-20714
α-helix211-22919
α-helix234-2374
β-strand238-244746
α-helix247-2493
β-strand252-254350
β-strand260-262350
α-helix265-28521
α-helix289-30719
α-helix315-3162
β-strand317151
β-strand323151
α-helix324-3252
α-helix328-3303
α-helix3371
α-helix338-3425
β-strand345-347333
β-strand350-354530
β-strand355-357352
β-strand365-369552
α-helix370-3767
α-helix378-38811
α-helix394-40310
α-helix406-41510
β-strand421-424430
α-helix431-4333
β-strand434-437430
β-strand438-442552
β-strand447-449352
α-helix454-4574
β-strand465-469530
α-helix474-4829
β-strand485130
α-helix486-4883
β-strand491153
β-strand498153
α-helix505-5139
β-strand526-527254
α-helix530-5389
β-strand547-5571154
β-strand563-5731154
α-helix574-5796
α-helix580-5823
α-helix5841
α-helix589-5913
α-helix598-61215
α-helix615-63521
α-helix641-6433
α-helix645-6473
α-helix650-66920
α-helix675-70127
β-strand703-707555
β-strand713-717555
α-helix721-7288
β-strand745156
β-strand748157
α-helix7531
β-strand754157
α-helix7551
β-strand759156
α-helix769-7735
α-helix776-80429
β-strand809-811358
β-strand820-822359
β-strand825-827360
β-strand828161
β-strand830-833460
α-helix836-8394
β-strand843162
β-strand844159
β-strand848-849263
β-strand856-858363
β-strand863162
α-helix866-87510
β-strand880-882359
α-helix885-8873
β-strand894-895258
α-helix896-8994
β-strand901164
β-strand908164
α-helix909-9102
α-helix915-92410
α-helix925-9295
β-strand949-951365
β-strand956-961661
β-strand965-967365
β-strand973-975365
β-strand980-985661
β-strand991-997761
α-helix10011
β-strand1002-1003265
β-strand1010-1011261
β-strand1016-1019465
β-strand1025-1028466
β-strand1033-1038667
β-strand1042166
β-strand1046-1050566
β-strand1057-1061566
β-strand1077-1081567
α-helix10861
β-strand1087167
α-helix10881
β-strand1089168
α-helix10901
β-strand1096168
β-strand1098-1100367
β-strand1106-1107266
β-strand1114-1115267
β-strand1120-1124566
α-helix1138-11458
α-helix1148-11503
α-helix1153-11553
β-strand1156169
β-strand1161-1165570
β-strand1172-1178770
β-strand1186-1191670
β-strand1203-1204270
β-strand1209169
α-helix1217-12237
α-helix1226-124318
α-helix1250-125910
β-strand1263-1268671
β-strand1279-1281371
α-helix1282-129413
β-strand1301-1304471
α-helix1319-13235
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-helix16-3217
α-helix35-373
α-helix46-5611
α-helix61-7919
Chain L: 29 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix97-1059
α-helix113-13523
α-helix138-15215
α-helix158-1614
α-helix215-23521
α-helix245-25814
α-helix263-28826
α-helix289-2935
α-helix294-2952
α-helix299-3068
α-helix314-3185
α-helix325-3284
α-helix330-3323
α-helix334-35118
α-helix355-38127
α-helix384-3918
α-helix392-3943
α-helix401-41818
α-helix427-44620
α-helix454-47421
α-helix477-4793
α-helix480-4878
α-helix491-50010
β-strand505-506250
β-strand510172
β-strand518172
α-helix519-5224
β-strand524132
α-helix531-54919
α-helix553-56311
α-helix573-5808
α-helix584-59916
α-helix607-6104

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA-directed RNA polymerase subunit betaIprotein1342Escherichia coliP0A8V2 (AlphaFold model)
DNA-directed RNA polymerase subunit omegaKprotein91Escherichia coliP0A800 (AlphaFold model)
Nascent RNARRNA5Escherichia coli
T7A1 promoter fragment non-template strandPDNA97Escherichia phage T7
DNA-directed RNA polymerase subunit alphaG, Hprotein329Escherichia coliP0A7Z4 (AlphaFold model)
DNA-directed RNA polymerase subunit beta'Jprotein1415Escherichia coliP0A8T7 (AlphaFold model)
RNA polymerase sigma factor RpoDLprotein616Escherichia coliP00579
T7A1 promoter fragment template strandQDNA97Escherichia phage T7
Sequence of entity 1 (I), FASTA
>9YMW_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 (K), FASTA
>9YMW_2 DNA-directed RNA polymerase subunit omega (chains K)
MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLIN
NQILDVRERQEQQEQEAAELQAVTAIAEGRR
Sequence of entity 3 (R), FASTA
>9YMW_3 Nascent RNA (chains R)
CCAUC
Sequence of entity 4 (P), FASTA
>9YMW_4 T7A1 promoter fragment non-template strand (chains P)
GCTTAATTTAAAATTTATCAAAAAGAGTATTGACTTAAAGTCTAACCTATAGGATACTTA
CAGCCATCGAGAGGGACACGGCGAATAGCCATCCCGG
Sequence of entity 5 (G, H), FASTA
>9YMW_5 DNA-directed RNA polymerase subunit alpha (chains G, H)
MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE
IDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGD
VEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPV
ERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP
EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL
TEIKDVLASRGLSLGMRLENWPPASIADE
Sequence of entity 6 (J), FASTA
>9YMW_6 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 7 (L), FASTA
>9YMW_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
>9YMW_8 T7A1 promoter fragment template strand (chains Q)
CCGGGATGGCTATTCGCCGTGTCCCTCTCGATGGCTGTAAGTATCCTATAGGTTAGACTT
TAAGTCAATACTCTTTTTGATAAATTTTAAATTAAGC

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg1
ZNZinc ionZn2
POPPyrophosphate 2-H2 O7 P21

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:

Browse structure collections

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