9YMV: DNA-directed RNA polymerase subunit beta

De novo initial transcribing RNA polymerase with pretranslocated 3-mer RNA / product complex (RPitc3). Determined by electron microscopy at 2.6 Å resolution. Released 29 Apr 2026.

Method
Electron microscopy
Resolution
2.6 Å
Organisms
Escherichia coli, Escherichia phage T7
Chains
9
Atoms
32,423
Mol. weight
522.48 kDa
Ligands
ATP, ZN, MG, POP
Released
29 Apr 2026

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

Secondary structure: helices and β-sheets

9YMV contains 187 α-helices and 209 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-strand12-18730
β-strand23-31930
α-helix35-4713
β-strand52-611031
β-strand74132
α-helix78-869
β-strand90-92333
β-strand97-105931
β-strand108-111432
α-helix112-1143
β-strand115131
α-helix116-1172
β-strand121-123333
β-strand129-133532
β-strand139-1501231
β-strand152-153234
α-helix155-1573
β-strand170-172331
β-strand175-176234
β-strand180-1891030
β-strand199-207930
α-helix213-22715
α-helix229-2324
Chain H: 5 helices, 16 β-strands
ElementResiduesLengthSheet
β-strand13-18635
β-strand23-31935
α-helix35-4915
β-strand52-60936
β-strand74137
α-helix78-869
β-strand90-92338
β-strand97-105936
β-strand108-110337
α-helix112-1143
β-strand115136
α-helix116-1172
β-strand121-123338
β-strand131-133337
β-strand139-1501236
β-strand152-153239
β-strand171-172236
β-strand175-176239
β-strand180-1901135
β-strand198-2071035
α-helix213-22614
Chain I: 65 helices, 89 β-strands
ElementResiduesLengthSheet
α-helix5-84
α-helix11-122
β-strand13-1421
α-helix19-202
α-helix23-264
α-helix29-3911
α-helix49-568
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-strand154-15965
β-strand172-17765
β-strand18016
β-strand184-18855
β-strand194-19855
β-strand204-20525
α-helix207-2126
α-helix217-2248
β-strand227-23377
β-strand236-23947
α-helix243-2464
β-strand25018
β-strand255-25739
β-strand260-26349
β-strand26818
α-helix271-2799
β-strand285-28737
α-helix289-2924
β-strand296-29727
β-strand301-303310
β-strand308-311410
β-strand315-31627
α-helix319-3268
β-strand332-33657
α-helix346-3538
α-helix359-37012
α-helix375-3762
α-helix378-38912
β-strand39616
α-helix398-40811
α-helix422-43716
β-strand451-45444
α-helix456-48126
α-helix496-50813
β-strand512-51433
α-helix515-5162
α-helix520-5278
β-strand529-53134
α-helix540-5423
α-helix550-5512
α-helix552-5543
β-strand558111
β-strand572-57434
β-strand575111
β-strand580-581212
β-strand587-595912
β-strand598-6071012
α-helix608-6114
β-strand616-617212
β-strand623113
β-strand628112
β-strand629113
β-strand633-638612
β-strand641-646612
α-helix647-6493
β-strand652-654312
α-helix665-6673
α-helix671-6733
α-helix676-68510
α-helix686-6883
β-strand689114
α-helix690-6912
β-strand700-70121
α-helix705-7117
β-strand716-717215
β-strand722-728716
β-strand731-736616
α-helix7371
α-helix7421
β-strand748-752516
β-strand757-758217
β-strand763118
β-strand764-765217
β-strand768-769215
β-strand776-777216
β-strand782-785415
β-strand789-790219
β-strand793-794219
β-strand798-804720
β-strand815-819520
α-helix820-8245
β-strand830-8411218
β-strand849121
β-strand865122
β-strand870123
β-strand871122
α-helix8721
β-strand876-877218
β-strand882-884323
β-strand887-889321
α-helix897-90610
α-helix908-9114
β-strand913-915321
β-strand918-919223
α-helix920-9212
β-strand926-9351018
α-helix943-98038
α-helix989-9913
α-helix994-9996
α-helix1011-103626
α-helix1042-10432
β-strand1046-10581318
β-strand1065-1067320
β-strand1073-1080820
α-helix1082-10843
β-strand1087124
α-helix10921
β-strand1093124
α-helix10941
β-strand1096-1098320
α-helix1100-11023
α-helix1110-113324
α-helix1138-115013
α-helix1161-11633
α-helix1168-11758
β-strand1182-118321
α-helix1192-120110
β-strand1209-1210220
β-strand1213124
α-helix12191
β-strand1220124
α-helix12211
β-strand1225-12341020
β-strand1235114
α-helix1239-12413
β-strand1244-1246325
β-strand1251126
β-strand1252127
β-strand1258126
α-helix12671
β-strand1268-1270328
α-helix1272-128110
α-helix1284-12918
α-helix1298-131013
α-helix1321-133212
β-strand1335-1340629
Chain J: 73 helices, 84 β-strands
ElementResiduesLengthSheet
β-strand19-24629
α-helix27-337
β-strand34-37440
β-strand44141
α-helix501
β-strand51141
α-helix521
α-helix59-624
α-helix78-803
α-helix831
β-strand84142
α-helix851
β-strand91142
α-helix95-995
β-strand102-1121140
α-helix115-1184
α-helix1221
α-helix123-1286
α-helix132-1398
β-strand144-148543
α-helix154-1552
β-strand159-160243
α-helix162-17110
β-strand177-179343
α-helix181-19111
α-helix194-20512
α-helix211-22919
α-helix234-2374
β-strand238-244740
α-helix247-2493
β-strand252-254344
β-strand260-262344
α-helix265-28521
α-helix289-30719
α-helix315-3162
β-strand317145
β-strand323145
α-helix324-3252
α-helix327-3315
α-helix3371
α-helix338-3425
β-strand345-347328
β-strand350-354525
β-strand355-357346
β-strand365-369546
α-helix370-3767
α-helix378-38710
α-helix394-40310
α-helix406-41510
β-strand421-424425
α-helix431-4333
β-strand434-437425
β-strand438-442546
β-strand447-449346
α-helix451-4533
α-helix454-4574
β-strand465-469525
α-helix474-4829
β-strand485125
α-helix486-4883
β-strand491147
β-strand498147
α-helix505-5139
β-strand526-527248
α-helix530-5389
β-strand547-5571148
β-strand563-5731148
α-helix574-5796
α-helix580-5823
α-helix5841
α-helix589-5913
α-helix598-61215
α-helix614-63522
α-helix645-6473
α-helix650-67021
α-helix675-70127
β-strand703-707549
β-strand713-717549
α-helix721-7288
β-strand745150
β-strand748151
α-helix7531
β-strand754151
α-helix7551
β-strand759150
α-helix769-80436
β-strand809-811352
β-strand820-822353
β-strand825-826254
β-strand828155
β-strand831-833354
α-helix836-8394
β-strand843156
β-strand844153
β-strand848-849257
β-strand856-858357
β-strand863156
α-helix866-87510
β-strand880-882353
α-helix885-8873
β-strand894-895252
α-helix896-8994
β-strand901158
β-strand908158
α-helix909-9102
α-helix915-92410
α-helix925-9284
β-strand949-952459
β-strand956160
β-strand957-961555
β-strand965-967359
β-strand973-975359
β-strand981-985555
β-strand991-996655
β-strand1002-1003259
β-strand1011160
β-strand1015-1019559
β-strand1025-1028461
β-strand1033162
β-strand1034-1038563
β-strand1042161
β-strand1046-1051661
β-strand1056-1061661
α-helix1062-10632
α-helix1069-10735
β-strand1077-1081563
β-strand1087163
β-strand1089164
α-helix10901
β-strand1096164
β-strand1098-1100363
β-strand1105-1107361
β-strand1115162
β-strand1120-1124561
α-helix1138-11458
α-helix1148-11503
β-strand1156165
β-strand1161-1165566
β-strand1172-1178766
β-strand1186-1191666
β-strand1203-1204266
β-strand1209165
α-helix1214-12163
α-helix1217-12237
α-helix1226-124217
α-helix1250-126011
β-strand1263-1268667
β-strand1279-1281367
α-helix1282-129413
β-strand1301-1304467
α-helix1309-13146
α-helix1319-13257
α-helix1328-133811
β-strand1341-1342229
α-helix1347-13526
α-helix1360-13623
α-helix1363-137311
Chain K: 4 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix7-137
α-helix16-3116
α-helix46-5611
α-helix61-7717
Chain L: 32 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix97-1059
α-helix109-1113
α-helix113-13523
α-helix138-15215
α-helix158-1614
α-helix215-23319
α-helix245-25814
α-helix263-29533
α-helix299-3068
α-helix313-3186
α-helix319-3213
α-helix325-3295
α-helix334-35118
α-helix355-38127
α-helix384-3929
α-helix401-41818
α-helix421-4233
α-helix427-44620
α-helix454-47421
α-helix477-4793
α-helix480-4878
α-helix491-4988
α-helix503-5042
β-strand505-506244
α-helix5091
β-strand510168
α-helix5111
β-strand518168
α-helix519-5224
β-strand524127
α-helix528-5303
α-helix531-54818
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)
T7A1 promoter fragment non-template strandPDNA97Escherichia phage T7
Nascent RNARRNA2Escherichia coli
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
>9YMV_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
>9YMV_2 DNA-directed RNA polymerase subunit omega (chains K)
MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLIN
NQILDVRERQEQQEQEAAELQAVTAIAEGRR
Sequence of entity 3 (P), FASTA
>9YMV_3 T7A1 promoter fragment non-template strand (chains P)
GCTTAATTTAAAATTTATCAAAAAGAGTATTGACTTAAAGTCTAACCTATAGGATACTTA
CAGCCATCGAGAGGGACACGGCGAATAGCCATCCCGG
Sequence of entity 4 (R), FASTA
>9YMV_4 Nascent RNA (chains R)
UC
Sequence of entity 5 (G, H), FASTA
>9YMV_5 DNA-directed RNA polymerase subunit alpha (chains G, H)
MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE
IDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGD
VEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPV
ERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP
EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL
TEIKDVLASRGLSLGMRLENWPPASIADE
Sequence of entity 6 (J), FASTA
>9YMV_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
>9YMV_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
>9YMV_8 T7A1 promoter fragment template strand (chains Q)
CCGGGATGGCTATTCGCCGTGTCCCTCTCGATGGCTGTAAGTATCCTATAGGTTAGACTT
TAAGTCAATACTCTTTTTGATAAATTTTAAATTAAGC

Ligands and cofactors

IDNameFormulaCopies
ATPAdenosine-5'-triphosphateC10 H16 N5 O13 P31
ZNZinc ionZn2
MGMagnesium ionMg1
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:

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