2024-07-24 REL PDBe PDBe PDBe 2022-07-05 2022-10-19 2022-10-19 2024-07-24 European Research Council (ERC) 679734 European Union French Infrastructure for Integrated Structural Biology (FRISBI) ANR-10-INBS-05 France Agence Nationale de la Recherche (ANR) ANR-10-LABX-0030-INRT France Agence Nationale de la Recherche (ANR) ANR-10-IDEX-0002-02 France Dey S Weixlbaumer A RNA polymerase, transcriptional pausing, transcription termination, regulatory RNA, TRANSCRIPTION Dey S Batisse C Shukla J Webster MW Takacs M Saint-Andre C Weixlbaumer A Mol.Cell US 82 3885 2022 36220101 doi:10.1016/j.molcel.2022.09.020 1097-2765 2168 MOCEFL 8abz FULLOVERLAP Escherichia coli RNA polymerase non-regulatory RNA complex - pause prone, closed clamp state Escherichia coli RNA polymerase non-regulatory RNA complex - pause prone, closed clamp state 0 1 2 3 4 5 6 7 Escherichia coli K-12 0.435 DNA-directed RNA polymerase subunit alpha Escherichia coli K-12 K12 0.036558679999999996 2 Escherichia coli BL21(DE3) LEVO MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILE ILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIH SEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLEN WPPASIADE P0A7Z4 2.7.7.6 DNA-directed RNA polymerase subunit beta Escherichia coli K-12 K12 0.150820875 1 Escherichia coli BL21(DE3) 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 K-12 0.155237672 1 Escherichia coli BL21(DE3) LEVO MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKH RGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQIL TEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILT VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSN KRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKM VEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDAN GELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVG IDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFN SIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRL VDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAV KVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKL SNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDM IDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDT LARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFE GERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQV EYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAG TGYAYHQDRMRRRAAGEAPAAPQVTAEDASASLAELLNAGLGGSDN C3SIA2 2.7.7.6 DNA-directed RNA polymerase subunit omega Escherichia coli K-12 K12 0.010249547 1 Escherichia coli BL21(DE3) LEVO MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAEL QAVTAIAEGRR P0A800 2.7.7.6 Non-template DNA Escherichia coli K-12 0.091015141 1 (DC)(DA)(DG)(DT)(DC)(DA)(DC)(DG)(DA)(DC)(DG)(DT)(DT)(DG)(DT)(DA)(DA)(DA)(DA)(DC) (DG)(DA)(DC)(DG)(DG)(DC)(DC)(DA)(DG)(DT)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DA)(DG)(DC) (DT)(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DA)(DA)(DA)(DA)(DA)(DT)(DA)(DA)(DA)(DT)(DT)(DT) (DC)(DC)(DT)(DT)(DA)(DA)(DA)(DG)(DT)(DT)(DC)(DA)(DC)(DT)(DA)(DA)(DC)(DT)(DT)(DA) (DT)(DG)(DA)(DT)(DG)(DT)(DA)(DG)(DT)(DG)(DA)(DG)(DC)(DT)(DT)(DT)(DT)(DT)(DA)(DT) (DA)(DC)(DC)(DC)(DA)(DT)(DA)(DA)(DA)(DA)(DT)(DG)(DT)(DA)(DC)(DT)(DA)(DT)(DT)(DG) (DG)(DT)(DA)(DC)(DT)(DT)(DT)(DA)(DC)(DA)(DT)(DT)(DA)(DA)(DT)(DG)(DA)(DA)(DC)(DT) (DT)(DT)(DA)(DA)(DG)(DT)(DA)(DC)(DA)(DT)(DC)(DA)(DT)(DA)(DA)(DG)(DC)(DC)(DC)(DA) (DT)(DC)(DG)(DA)(DG)(DA)(DG)(DG)(DG)(DA)(DC)(DA)(DC)(DG)(DG)(DG)(DG)(DA)(DA)(DA) (DC)(DA)(DC)(DC)(DA)(DC)(DC)(DA)(DT)(DG)(DC)(DT)(DT)(DA)(DT)(DA)(DA)(DT)(DA)(DA) (DT)(DT)(DC)(DT)(DG)(DC)(DC)(DG)(DG)(DA)(DG)(DC)(DG)(DA)(DC)(DC)(DG)(DC)(DA)(DC) (DT)(DG)(DT)(DG)(DG)(DT)(DT)(DT)(DA)(DC)(DC)(DA)(DG)(DA)(DT)(DG)(DG)(DC)(DG)(DT) (DG)(DT)(DG)(DT)(DC)(DC)(DC)(DA)(DA)(DT)(DC)(DT)(DT)(DT)(DC)(DA)(DC)(DA)(DA)(DC) (DA)(DT)(DT)(DA)(DG)(DC)(DG)(DA)(DG)(DA)(DA)(DG)(DG)(DC)(DT)(DT)(DT)(DT)(DT)(DT) (DG)(DT)(DT)(DT)(DT)(DT)(DA)(DG)(DT)(DC)(DA)(DC)(DG)(DG)(DC) DNA Non-regulatory RNA Escherichia coli 0.039226262 1 AUCGAGAGGGACACGGGGAAACACCACCAUGCUUAUAAUAAUUCUGCCGGAGCGACCGCACUGUGGUUUACCAGAUGGCG UGUGUCCCAAUCUUUCACAACAUUAGCGAGAAGGCUUUUUUG Template DNA Escherichia coli K-12 0.09118020299999999 1 (DG)(DC)(DC)(DG)(DT)(DG)(DA)(DC)(DT)(DA)(DA)(DA)(IGU)(IGU)(DC)(DA)(DA)(DA)(DA) (DA)(DA)(DG)(DC)(DC)(DT)(DT)(DC)(DT)(DC)(DG)(DC)(DT)(DA)(DA)(DT)(DG)(DT)(DT)(DG) (DT)(DG)(DA)(DA)(DA)(DG)(DA)(DT)(DT)(DG)(DG)(DG)(DA)(DC)(DA)(DC)(DA)(DC)(DG)(DC) (DC)(DA)(DT)(DC)(DT)(DG)(DG)(DT)(DA)(DA)(DA)(DC)(DC)(DA)(DC)(DA)(DG)(DT)(DG)(DC) (DG)(DG)(DT)(DC)(DG)(DC)(DT)(DC)(DC)(DG)(DG)(DC)(DA)(DG)(DA)(DA)(DT)(DT)(DA)(DT) (DT)(DA)(DT)(DA)(DA)(DG)(DC)(DA)(DT)(DG)(DG)(DT)(DG)(DG)(DT)(DG)(DT)(DT)(DT)(DC) (DC)(DC)(DC)(DG)(DT)(DG)(DT)(DC)(DC)(DC)(DT)(DC)(DT)(DC)(DG)(DA)(DT)(DG)(DG)(DG) (DC)(DT)(DT)(DA)(DT)(DG)(DA)(DT)(DG)(DT)(DA)(DC)(DT)(DT)(DA)(DA)(DA)(DG)(DT)(DT) (DC)(DA)(DT)(DT)(DA)(DA)(DT)(DG)(DT)(DA)(DA)(DA)(DG)(DT)(DA)(DC)(DC)(DA)(DA)(DT) (DA)(DG)(DT)(DA)(DC)(DA)(DT)(DT)(DT)(DT)(DA)(DT)(DG)(DG)(DG)(DT)(DA)(DT)(DA)(DA) (DA)(DA)(DA)(DG)(DC)(DT)(DC)(DA)(DC)(DT)(DA)(DC)(DA)(DT)(DC)(DA)(DT)(DA)(DA)(DG) (DT)(DT)(DA)(DG)(DT)(DG)(DA)(DA)(DC)(DT)(DT)(DT)(DA)(DA)(DG)(DG)(DA)(DA)(DA)(DT) (DT)(DT)(DA)(DT)(DT)(DT)(DT)(DT)(DG)(DG)(DT)(DA)(DC)(DC)(DG)(DA)(DG)(DC)(DT)(DC) (DG)(DA)(DA)(DT)(DT)(DC)(DA)(DC)(DT)(DG)(DG)(DC)(DC)(DG)(DT)(DC)(DG)(DT)(DT)(DT) (DT)(DA)(DC)(DA)(DA)(DC)(DG)(DT)(DC)(DG)(DT)(DG)(DA)(DC)(DT)(DG) DNA MAGNESIUM ION 2.4305e-05 1 MG ZINC ION 6.5409e-05 2 ZN singleParticle particle 12 8.0

20 mM Tris-glutamate pH 8.0, 50 mM K-glutamate, 10 mM Mg-glutamate, 0.001 mM ZnCl2, 2mM DTT

Quantifoil R1.2/1.3 GOLD GOLD HOLEY PLASMA CLEANING 30 OTHER ETHANE 95 283 FEI VITROBOT MARK IV

Quantifoil UltrAuFoil R1.2/1.3 300 mesh holey gold grids were plasma cleaned on a Model 1070 (Fischione Instruments) for 30 sec at 70% power and with an 80% Argon and 20% Oxygen mixture prior to the application of 0.004 ml of sample. Grids were plunge frozen into liquid ethane using a Vitrobot mark IV (FEI) with 95% chamber humidity at 283K..

The co-transcriptionally halted complexes for cryo-EM analysis were prepared in vitro by mixing E. coli RNAP holoenzyme with templates containing the DNA base analogue isoG. The RNAP ECs halted at the U-rich pause (G93). The complexes were prepared in 0.03 ml reactions and contained: 0.02 mM of E. coli RNAP, 0.080 mM of E. coli Sigma70, 0.02 mM of template DNA, 20 mM Tris-glutamate pH 8.0, 50 mM K-glutamate, 10 mM Mg-glutamate, 0.001 mM ZnCl2, 2mM DTT and 6 mM of each ATP, GTP, CTP and UTP. Initially, all the components except NTPs were added and incubated for 10 min at 310K. To allow transcription elongation, NTPs were added and the sample was incubated for 20 to 40 min at 310K. The final products were purified on a Superose 6 Increase 3.2/300 gel filtration column equilibrated in Glutamate buffer. Samples were concentrated to 10-12 mg/mL using an Amicon Ultra 0.5mL centrifugal filter unit (30 KDa MWCO). Before grid freezing, 8 mM of CHAPSO was added to freshly prepared sample to overcome preferred particle orientation.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.8 2.5 FEI TITAN KRIOS AUTOGRID HOLDER GATAN K3 (6k x 4k) 1 2.2 52.0 1 3.4 FSC 0.143 CUT-OFF cryoSPARC 3.3 180841 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC 3.3 cryoSPARC 3.3 6ALH PDB experimental model FLEXIBLE FIT map cross correlation REAL emd_15328_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 310.32 310.32 310.32 90.0 90.0 90.0 X Y Z -0.11370065 0.38467118 0.0008664145 0.015606192 0.86200005 0.86200005 0.86200005 AUTHOR ::::EMDATABANK.org::::EMD-15328:::: emd_15328_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 310.32 310.32 310.32 90.0 90.0 90.0 X Y Z -0.264615 0.5183443 0.0012121218 0.03346828 0.86200005 0.86200005 0.86200005 AUTHOR ::::EMDATABANK.org::::EMD-15328:::: emd_15328_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 310.32 310.32 310.32 90.0 90.0 90.0 X Y Z -0.24362946 0.5095041 0.0012169853 0.03359847 0.86200005 0.86200005 0.86200005 AUTHOR ::::EMDATABANK.org::::EMD-15328::::