Cryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme intermediate partially loaded complex

2024-05-15 REL PDBe PDBe PDBe 2018-05-04 2018-06-06 2018-07-04 2024-05-15 Biotechnology and Biological Sciences Research Council BB/N007816 United Kingdom Cryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme intermediate partially loaded complex Glyde R Ye FZ transcription initiation, DNA loading, transcription bubble, sigma factor, TRANSCRIPTION Glyde R Ye F Jovanovic M Kotta-Loizou I Buck M Zhang X Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation. Mol. Cell US 70 1111 1120.e3 2018 29932903 doi:10.1016/j.molcel.2018.05.021 1097-4164 2168 MOCEFL EMD-4397 other EM volume 6gh6 FULLOVERLAP Cryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme intermediate partially loaded complex Cryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme intermediate partially loaded complex 0 1 2 3 4 5 6 7 0.490 RNA polymerase 1 1 2 3 4 Escherichia coli K-12 sigma factor 54, 1 5 Klebsiella pneumoniae DNA 1 6 7 Klebsiella pneumoniae DNA-directed RNA polymerase subunit alpha Escherichia coli (strain K12) 0.036558679999999996 2 Escherichia coli 'BL21-Gold(DE3)pLysS AG' LEVO MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILE ILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIH SEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLEN WPPASIADE P0A7Z4 2.7.7.6 DNA-directed RNA polymerase subunit beta Escherichia coli (strain K12) 0.150820875 1 Escherichia coli 'BL21-Gold(DE3)pLysS AG' LEVO MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVF DVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSD KGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQME LVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLD LLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAV GRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLS LGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCP IETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKG ESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKR GGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNM RVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGG DILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDL SEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGD DLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMA AKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLK LGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEA YGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE P0A8V2 2.7.7.6 DNA-directed RNA polymerase subunit beta' Escherichia coli (strain K12) 0.15536678099999998 1 Escherichia coli 'BL21-Gold(DE3)pLysS AG' LEVO MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKH RGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQIL TEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILT VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSN KRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKM VEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDAN GELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVG IDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFN SIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRL VDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAV KVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKL SNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDM IDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDT LARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFE GERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQV EYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAG TGYAYHQDRMRRRAAGEAPAAPQVTAEDASASLAELLNAGLGGSDNE P0A8T7 2.7.7.6 DNA-directed RNA polymerase subunit omega Escherichia coli (strain K12) 0.010249547 1 Escherichia coli 'BL21-Gold(DE3)pLysS AG' LEVO MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAEL QAVTAIAEGRR P0A800 2.7.7.6 RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor Klebsiella pneumoniae 0.05473508999999999 1 Escherichia coli 'BL21-Gold(DE3)pLysS AG' LEVO MGSSHHHHHHSSGLVPRGSHMKQGLQLRLSQQLAMTPQLQQAIRLLQLSTLELQQELQQALESNPLLEQTDLHDEVEAKE VEDRESLDTVDALEQKEMPDELPLDASWDEIYTAGTPSGNGVDYQDDELPVYQGETTQTLQDYLMWQVELTPFTDTDRAI ATSIVDAVDDTGYLTIQIEDIVDSIGDDEIGLEEVEAVLKRIQRFDPVGVAAKDLRDCLLIQLSQFAKETPWLEEARLII SDHLDLLANHDFRTLMRVTRLKEEVLKEAVNLIQSLDP(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)IPRLKINQQYAAMGNSARNDADGQF IRSNLQEARWLIKSLESANDTLLRVSRCIVEQQQAFFEQGEEYMKPMVLADIAQAVEMHESTISRVTTQKYLHSPRGIF (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) EASSTAIRALVKKLIAAENPAKPLSDSKLTSMLSEQGIMVARRTVAKYRESLSIPPSNQRKQLV A0A0J4U551 A0A0J4U551 A0A0J4U551 nifH promoter non-tmeplate DNA Klebsiella pneumoniae 0.019487436 1 (DG)(DA)(DG)(DA)(DC)(DG)(DG)(DC)(DT)(DG)(DG)(DC)(DA)(DC)(DG)(DA)(DC)(DT)(DT)(DT) (DT)(DG)(DC)(DA)(DC)(DT)(DC)(DG)(DA)(DC)(DT)(DA)(DA)(DA)(DG)(DG)(DG)(DG)(DC)(DG) (DC)(DG)(DC)(DA)(DT)(DG)(DC)(DT)(DG)(DT)(DT)(DG)(DC)(DG)(DC)(DA)(DT)(DT)(DC)(DA) (DT)(DG)(DT) DNA nifH promoter template DNA Klebsiella pneumoniae 0.01940441 1 (DA)(DC)(DA)(DT)(DG)(DA)(DA)(DT)(DG)(DC)(DG)(DC)(DA)(DA)(DC)(DA)(DG)(DC)(DA)(DT) (DG)(DC)(DG)(DC)(DG)(DC)(DC)(DC)(DA)(DG)(DG)(DG)(DC)(DT)(DG)(DA)(DT)(DC)(DG)(DT) (DG)(DC)(DA)(DA)(DA)(DA)(DG)(DT)(DC)(DG)(DT)(DG)(DC)(DC)(DA)(DG)(DC)(DC)(DG)(DT) (DC)(DT)(DC) DNA singleParticle particle 0.5 8.0 10.0 Tris-HCL Tris hydrochloride 150.0 NaCL sodium chloride 10.0 MgCl2 magnesium chloride Quantifoil R1.2/1.3 COPPER ETHANE 95 277 FEI VITROBOT MARK IV FEI TITAN KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) COUNTING 48.0 1 6GFW C1 4.1 FSC 0.143 CUT-OFF 53709 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_0002.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 276.48 276.48 276.48 90.0 90.0 90.0 X Y Z -0.081265144 0.19144611 0.0005381993 0.0061218822 1.08 1.08 1.08 0.016 EMDB ::::EMDATABANK.org::::EMD-0002:::: RIGID BODY FIT REAL