2025-07-02 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY em_admin em_software pdbx_entry_details _em_admin.last_update _em_software.name _pdbx_entry_details.has_protein_modification EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name PDBe PDBe 2023-12-10 2024-01-17 2024-01-17 2025-07-02 UK Research and Innovation (UKRI) BB/M011178/1 United Kingdom Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 7nt complex Gao F Zhang X initiation, rna polymerase, sigma54, TRANSCRIPTION Gao F Ye F Zhang B Cronin N Buck M Zhang X Structural basis of sigma 54 displacement and promoter escape in bacterial transcription. Proc.Natl.Acad.Sci.USA US 121 e2309670120 e2309670120 2024 38170755 doi:10.1073/pnas.2309670120 1091-6490 0040 PNASA6 8rec FULLOVERLAP RNA polymerase-sigma54 initial transcribing complex - 7nt complex RNA polymerase-sigma54 initial transcribing complex - 7nt complex 0 1 2 3 4 5 6 7 8 Escherichia coli K-12 DNA (46-MER) Klebsiella oxytoca 0.014059012 1 (DG)(DC)(DT)(DG)(DG)(DC)(DA)(DC)(DG)(DA)(DC)(DT)(DT)(DT)(DT)(DG)(DC)(DA)(DC)(DT) (DC)(DG)(DA)(DA)(DT)(DA)(DT)(DC)(DT)(DC)(DA)(DT)(DG)(DC)(DT)(DG)(DT)(DT)(DG)(DC) (DA)(DC)(DA)(DT)(DT)(DC) DNA RNA (5'-R(P*GP*CP*CP*GP*CP*GP*A)-3') Klebsiella oxytoca 0.002235411 1 GCCGCGA DNA (51-MER) Klebsiella oxytoca 0.015800135 1 (DG)(DA)(DA)(DT)(DG)(DT)(DG)(DC)(DA)(DA)(DC)(DA)(DG)(DC)(DA)(DT)(DG)(DA)(DT)(DC) (DG)(DC)(DG)(DG)(DC)(DA)(DA)(DG)(DC)(DT)(DG)(DC)(DG)(DT)(DG)(DC)(DA)(DA)(DA)(DA) (DG)(DT)(DC)(DG)(DT)(DG)(DC)(DC)(DA)(DG)(DC) DNA DNA-directed RNA polymerase subunit alpha Escherichia coli K-12 0.035726788999999995 2 Escherichia coli K-12 LEVO SVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILL NLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEE DERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVK EEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPP A P0A7Z4 2.7.7.6 DNA-directed RNA polymerase subunit beta Escherichia coli K-12 0.15069174999999999 1 Escherichia coli K-12 LEVO MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVF DVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSD KGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQME LVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLD LLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAV GRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLS LGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCP IETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKG ESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKR GGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNM RVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGG DILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDL SEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGD DLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMA AKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLK LGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEA YGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELED P0A8V2 DNA-directed RNA polymerase subunit beta' Escherichia coli K-12 0.152040266 1 Escherichia coli K-12 LEVO LLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGV ICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEE QYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLP VLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRP LKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVER EEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARAL MMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGEL VAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDD MVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFNSIY MMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDV AQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVR SVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKLSNV KSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDG QTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLAR IPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGER VERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYS RVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGY AYHQDRMRRRAAG P0A8T7 DNA-directed RNA polymerase subunit omega Escherichia coli K-12 0.008449504 1 Escherichia coli K-12 LEVO ARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQ P0A800 2.7.7.6 RNA polymerase sigma-54 factor Klebsiella oxytoca 0.03901093 1 Klebsiella oxytoca LEVO TAGTPSGNGVDYQDDELPVYQGETTQSLQDYLMWQVELTPFTDTDRAIATSIVDAVDDTGYLTIQIEDIVDSIGDDEIGL EEVEAVLKRIQRFDPVGVAAKDLRDCLLIQLSQFAKETPWLEEARLIISDHLDLLANHDFRTLMRVTRLKEEVLKEAVNL IQSLDPRPGQSIQTGEPEYVIPDVLVRKVNDRWVVELNSDSRWLIKSLESANDTLLRVSRCIVEQQQAFFEQGEEYMKPM VLADIAQAVEMHESTISRVTTQKYLHSPRGIFELKYFFSSHVNTEGGGEASSTAIRALVKKLIAAENPAKPLSDSKLTSM LSEQGIMVARRTVAKYRESLSIPPSNQ MAGNESIUM ION 2.4305e-05 1 MG ZINC ION 6.5409e-05 2 ZN singleParticle particle 8.0 ETHANE TFS KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 1.0 3.0 GATAN K3 (6k x 4k) 30.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION EMD-0001 3.5 FSC 0.143 CUT-OFF 46380 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_19082.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 211.99998 211.99998 211.99998 90.0 90.0 90.0 X Y Z -0.015447679 0.03863163 0.000040050207 0.002616108 1.06 1.06 1.06 0.0077 AUTHOR emd_19082_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 211.99998 211.99998 211.99998 90.0 90.0 90.0 X Y Z -0.16156709 0.24305248 0.000356127 0.009510545 1.06 1.06 1.06 AUTHOR Locally sharpened map emd_19082_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 211.99998 211.99998 211.99998 90.0 90.0 90.0 X Y Z -0.029327998 0.051451724 0.00004873849 0.003852154 1.06 1.06 1.06 AUTHOR emd_19082_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 211.99998 211.99998 211.99998 90.0 90.0 90.0 X Y Z -0.027482467 0.050485868 0.000050054732 0.0038515448 1.06 1.06 1.06 AUTHOR