transcription complex paused at ops site and bound to autoinhibited RfaH, not fully complementary scaffold

2024-11-20 REL PDBe PDBe PDBe 2023-06-15 2024-04-24 2024-04-24 2024-11-20 German Research Foundation (DFG) WA 1126/11-1 Germany German Research Foundation (DFG) INST 130/1064-1 FUGG Germany German Research Foundation (DFG) Ro617/21-1 Germany transcription complex paused at ops site and bound to autoinhibited RfaH, not fully complementary scaffold Zuber PK Said N Hilal T Loll B Wahl MC Knauer SH transcription complex, RfaH, ops, pausing, TRANSCRIPTION Zuber PK Said N Hilal T Wang B Loll B Gonzalez-Higueras J Ramirez-Sarmiento CA Belogurov GA Artsimovitch I Wahl MC Knauer SH Concerted transformation of a hyper-paused transcription complex and its reinforcing protein. Nat Commun UK 15 3040 3040 2024 38589445 doi:10.1038/s41467-024-47368-4 2041-1723 8pfg FULLOVERLAP transcription complex paused at ops site, assembled on not fully complementary nucleic acid scaffold, bound to disulfide-bridged (autoinhibited) RfaH transcription complex paused at ops site, assembled on not fully complementary nucleic acid scaffold, bound to disulfide-bridged (autoinhibited) RfaH 0 1 2 3 4 5 6 7 8 0.417 Transcription complex 1 1 2 3 4 5 Escherichia coli DNA and RNA 1 6 7 8 Escherichia coli Transcription antitermination protein RfaH Escherichia coli 0.018531449 1 Escherichia coli BL21(DE3) LEVO GHMQSWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLCPNYLFVEFDPEVIHTTTINATRGVSHF VRFGASPAIVPSAVIHQLSVYKPKDIVDPATPYPGDKVIITEGAFEGFQAIFTEPDGEARCMLLLNLINKEIKHSVKNTE FRKL P0AFW0 DNA-directed RNA polymerase subunit beta Escherichia coli 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 0.156504969 1 Escherichia coli BL21(DE3) LEVO VKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKH RGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQIL TEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILT VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSN KRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKM VEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDAN GELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVG IDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFN SIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRL VDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAV KVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKL SNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDM IDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDT LARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFE GERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQV EYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAG TGYAYHQDRMRRRAAGEAPAAPQVTAEDASASLAELLNAGLGGSDNELEVHHHHHH P0A8T7 2.7.7.6 DNA-directed RNA polymerase subunit omega Escherichia coli 0.010249547 1 Escherichia coli BL21(DE3) LEVO MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAEL QAVTAIAEGRR P0A800 2.7.7.6 DNA-directed RNA polymerase subunit alpha Escherichia coli 0.036558679999999996 2 Escherichia coli BL21(DE3) LEVO MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILE ILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIH SEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLEN WPPASIADE P0A7Z4 2.7.7.6 RNA Escherichia coli 0.005382189 1 UCUAUAUGUCAGCGUGU template DNA Escherichia coli 0.012446004 1 (DG)(DG)(DA)(DA)(DG)(DA)(DT)(DC)(DG)(DA)(DA)(DA)(DA)(DA)(DA)(DG)(DC)(DA)(DC)(DA) (DC)(DG)(DC)(DT)(DG)(DA)(DC)(DC)(DC)(DG)(DC)(DG)(DT)(DG)(DG)(DT)(DG)(DG)(DT)(DG) DNA non-template DNA Escherichia coli 0.012207801999999999 1 (DC)(DA)(DC)(DC)(DA)(DC)(DC)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DC)(DG)(DG)(DT)(DA)(DG) (DC)(DG)(DT)(DG)(DC)(DT)(DT)(DT)(DT)(DT)(DT)(DC)(DG)(DA)(DT)(DC)(DT)(DT)(DC)(DC) DNA ZINC ION 6.5409e-05 1 ZN MAGNESIUM ION 2.4305e-05 1 MG singleParticle particle 3.3 7.5 20.0 Tris 120.0 KOAc 5.0 Mg(OAc)2 0.01 ZnCl2 Quantifoil R1.2/1.3 COPPER 200 CARBON HOLEY GLOW DISCHARGE 60 ETHANE 100 283 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 0.8 2.0 96000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON III (4k x 4k) COUNTING 1 4979 40.57 42.0 1 1519652 1 C1 BACK PROJECTION 3.1 FSC 0.143 CUT-OFF cryoSPARC 3.2.0 509867 RANDOM ASSIGNMENT cryoSPARC 3.2.0 MAXIMUM LIKELIHOOD cryoSPARC 3.2.0 1 cryoSPARC 3.2.0 emd_17646.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 319.488 319.488 319.488 90.0 90.0 90.0 X Y Z 0.0 2.0899193 0.00633846 0.04840867 0.832 0.832 0.832 0.25 AUTHOR ::::EMDATABANK.org::::EMD-17646:::: FLEXIBLE FIT REAL 121.0 emd_17646_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 319.488 319.488 319.488 90.0 90.0 90.0 X Y Z -0.87746084 2.2654026 0.001178982 0.08264983 0.832 0.832 0.832 AUTHOR ::::EMDATABANK.org::::EMD-17646:::: emd_17646_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 319.488 319.488 319.488 90.0 90.0 90.0 X Y Z -0.83186877 2.090242 0.0011768545 0.08279652 0.832 0.832 0.832 AUTHOR ::::EMDATABANK.org::::EMD-17646::::