7SZK: 27a

Cryo-EM structure of 27a bound to E. coli RNAP and rrnBP1 promoter complex. Determined by electron microscopy at 2.94 Å resolution. Released 13 Jul 2022.

Method
Electron microscopy
Resolution
2.94 Å
Organism
Escherichia coli K-12
Chains
8
Atoms
29,759
Mol. weight
500.65 kDa
Ligands
MG, D9X, ZN
Released
13 Jul 2022

Explore 7SZK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SZK contains 162 α-helices and 225 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 A: 6 helices, 17 β-strands

ElementResiduesLengthSheet
β-strand1311
β-strand1711
β-strand23-3191
α-helix35-4915
β-strand53-6192
β-strand7413
α-helix78-869
β-strand9014
β-strand97-10592
β-strand108-11143
α-helix112-1143
β-strand11512
α-helix116-1172
β-strand12314
β-strand129-13353
β-strand139-149112
β-strand152-15325
α-helix155-1606
β-strand171-17222
β-strand175-17625
β-strand180-189101
β-strand199-20791
α-helix213-23220
Chain B: 7 helices, 18 β-strands
ElementResiduesLengthSheet
α-helix9-113
β-strand13-1756
β-strand24-3186
α-helix35-4915
β-strand52-61107
β-strand7418
α-helix78-869
β-strand90-9129
β-strand98-10587
β-strand108-11148
α-helix112-1143
β-strand11517
α-helix116-1172
β-strand122-12329
β-strand129-13358
β-strand139-150127
β-strand152-153210
α-helix155-1606
β-strand170-17237
β-strand175-176210
β-strand183-18976
β-strand192111
β-strand195111
β-strand199-20576
α-helix213-23220
Chain C: 58 helices, 101 β-strands
ElementResiduesLengthSheet
α-helix5-95
α-helix11-122
β-strand13-14212
α-helix19-202
α-helix29-3911
α-helix49-568
α-helix571
β-strand59-60213
β-strand66-751013
α-helix82-887
β-strand93-1041213
β-strand115-117313
β-strand122-128713
α-helix129-1302
β-strand136-137214
β-strand142-145414
β-strand148-151415
α-helix1521
β-strand154-155216
β-strand158116
α-helix164-1663
β-strand173-177516
β-strand180117
α-helix182-1832
β-strand184-187416
β-strand195-197316
β-strand205116
α-helix207-2126
α-helix217-2248
β-strand229-230218
β-strand240118
α-helix244-2463
β-strand250119
β-strand257120
β-strand260120
β-strand268119
α-helix271-28010
β-strand284118
α-helix289-2924
β-strand296121
β-strand297122
β-strand301123
β-strand311123
β-strand316121
α-helix319-3279
β-strand333-334218
β-strand335122
α-helix346-3538
α-helix359-37012
α-helix378-38912
β-strand396117
α-helix399-40810
α-helix422-43716
β-strand451-454415
α-helix456-48126
α-helix496-50712
β-strand512-514314
α-helix515-5162
α-helix520-5278
α-helix540-5423
α-helix552-5543
β-strand558124
β-strand575124
β-strand580-581225
β-strand587-588225
β-strand589-594626
β-strand598127
β-strand599-606826
α-helix608-6136
β-strand616-617226
β-strand623128
β-strand628127
β-strand629128
β-strand634-637426
β-strand642-645426
α-helix647-6493
β-strand652-654326
α-helix663-6664
α-helix671-6733
β-strand674129
α-helix676-68510
α-helix686-6883
β-strand689130
β-strand700-701212
α-helix705-7117
β-strand716-717231
β-strand722-728732
β-strand731-736632
β-strand749-752432
β-strand757-758233
β-strand763134
β-strand764-765233
β-strand768-769231
β-strand776-777232
β-strand782-785431
β-strand789-790235
β-strand793-794235
β-strand798-804736
β-strand816-819436
α-helix821-8244
β-strand830-8411234
β-strand842137
β-strand847137
β-strand849138
α-helix859-8624
β-strand865139
β-strand870140
β-strand871139
α-helix8721
β-strand876-877234
β-strand882-884340
β-strand887-889338
α-helix897-90610
β-strand913-915338
β-strand918-919240
α-helix920-9212
β-strand926-9351034
β-strand936141
α-helix943-98038
α-helix986-9916
α-helix994-9996
α-helix1006-103732
β-strand1040141
β-strand1046-10581334
α-helix1059-10602
β-strand1065142
β-strand1066-1067243
β-strand1075142
β-strand1076-1080536
α-helix1082-10843
β-strand1087144
β-strand1093144
β-strand1096-1098336
α-helix1100-11023
β-strand1108129
α-helix1110-113324
α-helix1138-115013
α-helix1167-117610
β-strand1182-1183212
α-helix1192-120110
β-strand1209-1210236
β-strand1213144
α-helix12191
β-strand1220144
α-helix12211
β-strand1225-1232836
β-strand1233-1234243
β-strand1235130
α-helix1239-12413
β-strand1244-1246345
β-strand1251146
β-strand1252147
β-strand1258146
β-strand1268-1269248
α-helix1272-12809
α-helix1284-12929
α-helix1298-131013
α-helix1321-133212
β-strand1335-1339549
Chain D: 63 helices, 83 β-strands
ElementResiduesLengthSheet
β-strand20-24549
α-helix27-337
β-strand37150
β-strand44151
β-strand51151
α-helix521
β-strand84152
β-strand91152
α-helix95-995
β-strand103-1121050
α-helix115-1184
α-helix123-1275
α-helix132-1398
β-strand144-146353
β-strand159-160253
α-helix162-17110
β-strand178-179253
α-helix182-19110
α-helix194-20714
α-helix211-22919
α-helix234-2374
β-strand238-244750
α-helix247-2493
α-helix2531
β-strand254154
α-helix2551
β-strand260154
β-strand261-262255
α-helix264-28522
α-helix289-30719
α-helix3151
β-strand316156
α-helix3171
β-strand323156
α-helix3241
α-helix327-3315
α-helix337-3404
β-strand346-347248
β-strand350-356745
β-strand365-369545
α-helix370-38718
α-helix394-40310
α-helix406-41510
β-strand421-424445
α-helix431-4333
β-strand434-442945
β-strand446-448345
α-helix451-4533
α-helix454-4574
β-strand465-469545
α-helix474-48310
β-strand485145
β-strand491157
β-strand498157
α-helix505-5139
β-strand526-527258
α-helix530-53910
β-strand547-5561058
β-strand564-5731058
α-helix574-5796
α-helix589-5913
α-helix598-61114
α-helix615-63521
α-helix641-6433
α-helix645-6473
α-helix650-66920
α-helix675-70329
β-strand706-708359
β-strand713-715359
α-helix721-7288
α-helix734-7418
β-strand748160
β-strand754160
α-helix769-80335
β-strand808161
β-strand809-811362
β-strand820-822363
β-strand825-827364
β-strand828165
β-strand830-833464
α-helix835-8395
β-strand843166
β-strand844163
α-helix8471
β-strand848-849267
α-helix8501
β-strand856-858367
β-strand863166
α-helix866-8749
β-strand880-882363
α-helix885-8873
β-strand894-895262
α-helix896-8994
β-strand914161
α-helix915-92410
α-helix925-9295
β-strand949-951368
β-strand956169
β-strand959-961370
β-strand965-967371
β-strand973-975371
β-strand980-983470
β-strand985172
β-strand991172
β-strand994165
β-strand995-997370
β-strand1002-1003268
β-strand1011169
β-strand1016-1019468
β-strand1033173
β-strand1035-1038474
β-strand1042175
β-strand1046175
β-strand1050176
β-strand1057176
β-strand1077-1080474
β-strand1081177
β-strand1087177
β-strand1089178
α-helix10901
β-strand1096178
β-strand1098174
α-helix11101
β-strand1115173
α-helix11161
α-helix1138-11469
α-helix1153-11553
β-strand1156179
β-strand1161-1165580
β-strand1175-1178480
β-strand1187-1188280
β-strand1203-1204280
β-strand1209179
α-helix1217-12248
α-helix1226-124217
α-helix1250-126011
β-strand1263-1266481
β-strand1277-1279381
α-helix1280-129213
β-strand1302-1304381
α-helix1309-13146
α-helix1319-13257
α-helix1328-133811
β-strand1341-1342249
α-helix1347-13537
α-helix1363-137210
Chain E: 5 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix7-126
α-helix19-3113
α-helix40-412
α-helix46-5510
α-helix61-7616
Chain F: 23 helices, 6 β-strands
ElementResiduesLengthSheet
α-helix97-10711
α-helix113-13624
α-helix140-15213
α-helix158-1614
β-strand162-165482
α-helix214-23320
α-helix244-25815
β-strand259-261382
α-helix263-29533
α-helix299-3068
α-helix314-3218
α-helix325-35127
α-helix355-39137
α-helix401-41717
α-helix427-44519
α-helix454-47421
α-helix480-4867
α-helix493-4997
α-helix5041
β-strand505-506255
β-strand510183
β-strand518183
α-helix519-5224
β-strand524147
α-helix531-55020
α-helix553-56210
α-helix573-5797
α-helix585-59915
α-helix605-6106

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA-directed RNA polymerase subunit alphaA, Bprotein329Escherichia coli K-12P0A7Z4 (AlphaFold model)
DNA-directed RNA polymerase subunit betaCprotein1342Escherichia coli K-12P0A8V2 (AlphaFold model)
DNA-directed RNA polymerase subunit beta'Dprotein1407Escherichia coli K-12P0A8T7 (AlphaFold model)
DNA-directed RNA polymerase subunit omegaEprotein91Escherichia coli K-12P0A800 (AlphaFold model)
RNA polymerase sigma factor RpoDFprotein613Escherichia coli K-12P00579
DNA (5'-d(p*cp*tp*cp*gp*tp*ap*gp*ap*gp*tp*cp*cp*gp*tp*gp*tp*cp*a)-3')XDNA64Escherichia coli K-12
DNA (5'-d(p*cp*tp*cp*gp*tp*ap*gp*ap*gp*tp*cp*cp*gp*tp*gp*tp*cp*a)-3')YDNA64Escherichia coli K-12
Sequence of entity 1 (A, B), FASTA
>7SZK_1 DNA-directed RNA polymerase subunit alpha (chains A, B)
MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE
IDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGD
VEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPV
ERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP
EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL
TEIKDVLASRGLSLGMRLENWPPASIADE
Sequence of entity 2 (C), FASTA
>7SZK_2 DNA-directed RNA polymerase subunit beta (chains C)
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 (D), FASTA
>7SZK_3 DNA-directed RNA polymerase subunit beta' (chains D)
MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCAR
IFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSL
PSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDEFDAKM
GAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILT
VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQ
EAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPY
LRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHP
VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA
RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSG
LASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKA
ISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAE
VAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFN
SIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGAR
KGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVL
GRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYG
RDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKL
SNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANW
DPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKI
VDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDITGGLPR
VADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFE
GERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQM
LRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFI
SAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAGEAPA
APQVTAEDASASLAELLNAGLGGSDNE
Sequence of entity 4 (E), FASTA
>7SZK_4 DNA-directed RNA polymerase subunit omega (chains E)
MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLIN
NQILDVRERQEQQEQEAAELQAVTAIAEGRR
Sequence of entity 5 (F), FASTA
>7SZK_5 RNA polymerase sigma factor RpoD (chains F)
MEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAP
DADDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA
KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATH
VGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGR
SHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKK
NFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKD
INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE
YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP
EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESL
RAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRH
PSRSEVLRSFLDD
Sequence of entity 6 (X), FASTA
>7SZK_6 DNA (5'-D(P*CP*TP*CP*GP*TP*AP*GP*AP*GP*TP*CP*CP*GP*TP*GP*TP*CP*A)-3') (chains X)
ATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGACTCTA
CGAG
Sequence of entity 7 (Y), FASTA
>7SZK_7 DNA (5'-D(P*CP*TP*CP*GP*TP*AP*GP*AP*GP*TP*CP*CP*GP*TP*GP*TP*CP*A)-3') (chains Y)
CTCGTAGAGTCCGTGTCAGTGGTGGCGCATTATAGGGAGTTATTCCGGCCTGACAAGAGG
AAAT

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg1
D9X(2S,7R,7aR,13aP,16Z,18E,20S,21S,22R,23R,24R,25S,26R,27S,28E)-5,21,23-trihydroxy…C63 H81 N5 O141
ZNZinc ionZn2

Primary citation

Optimization of Benzoxazinorifamycins to Improve Mycobacterium tuberculosis RNA Polymerase Inhibition and Treatment of Tuberculosis. Rajeswaran, W., Ashkar, S.R., Lee, P.H. et al. ACS Infect Dis (2022) 8:1422-1438. DOI 10.1021/acsinfecdis.1c00636 · PubMed

Other PDB entries of the same protein (UniProt P0A7Z4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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