Cryo-EM structure of E. coli RNAP-DNA elongation complex 2 (RDe2) in EcmrR-dependent transcription

2024-03-06 REL RCSB RCSB RCSB 2020-06-28 2021-04-07 2021-04-07 2024-03-06 Cryo-EM structure of E. coli RNAP-DNA elongation complex 2 (RDe2) in EcmrR-dependent transcription Yang Y Liu C Transcriptional factor, TRANSCRIPTION, TRANSFERASE-DNA complex, promoter escape, multidrug recognition Yang Y Liu C Zhou W Shi W Chen M Zhang B Schatz DG Hu Y Liu B Structural visualization of transcription activated by a multidrug-sensing MerR family regulator. Nat Commun UK 12 2702 2702 2021 33976201 doi:10.1038/s41467-021-22990-8 2041-1723 EMD-22234 other EM volume EMD-22235 other EM volume EMD-22236 other EM volume EMD-22237 other EM volume EMD-22245 other EM volume EMD-22246 other EM volume EMD-22247 other EM volume EMD-22248 other EM volume 6xln FULLOVERLAP E. coli RNAP-DNA elongation complex 2 (RDe2) E. coli RNAP-DNA elongation complex 2 (RDe2) 0 1 2 3 4 5 6 7 Escherichia coli O157:H7 DNA-directed RNA polymerase subunit alpha Escherichia coli O157:H7 0.036558679999999996 2 Escherichia coli O157:H7 LEVO MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILE ILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIH SEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLEN WPPASIADE P0A7Z6 2.7.7.6 DNA-directed RNA polymerase subunit beta Escherichia coli O157:H7 0.150820875 1 Escherichia coli O157:H7 LEVO MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVF DVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSD KGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQME LVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLD LLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAV GRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLS LGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCP IETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKG ESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKR GGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNM RVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGG DILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDL SEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGD DLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMA AKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLK LGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEA YGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE B7MIX3 2.7.7.6 DNA-directed RNA polymerase subunit beta' Escherichia coli O157:H7 0.15536678099999998 1 Escherichia coli O157:H7 LEVO MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKH RGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQIL TEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILT VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSN KRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKM VEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDAN GELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVG IDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFN SIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRL VDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAV KVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKL SNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDM IDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDT LARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFE GERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQV EYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAG TGYAYHQDRMRRRAAGEAPAAPQVTAEDASASLAELLNAGLGGSDNE P0A8T8 2.7.7.6 DNA-directed RNA polymerase subunit omega Escherichia coli O157:H7 0.010249547 1 Escherichia coli O157:H7 LEVO MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAEL QAVTAIAEGRR B7MFL0 2.7.7.6 synthetic non-template strand DNA (54-MER) Escherichia coli O157:H7 0.016718657999999997 1 (DG)(DC)(DC)(DT)(DT)(DG)(DA)(DC)(DC)(DC)(DT)(DC)(DC)(DC)(DC)(DT)(DA)(DA)(DG)(DG) (DG)(DG)(DA)(DG)(DG)(DG)(DT)(DT)(DT)(DA)(DG)(DA)(DT)(DT)(DG)(DT)(DG)(DT)(DG)(DC) (DA)(DG)(DT)(DC)(DT)(DG)(DA)(DC)(DG)(DC)(DG)(DG)(DC)(DG) DNA synthetic template strand DNA (54-MER) Escherichia coli O157:H7 0.016563606999999998 1 (DC)(DG)(DC)(DC)(DG)(DC)(DG)(DT)(DC)(DA)(DG)(DA)(DC)(DT)(DG)(DC)(DA)(DC)(DA)(DC) (DA)(DA)(DT)(DC)(DT)(DA)(DA)(DA)(DC)(DC)(DC)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DA)(DG) (DG)(DG)(DG)(DA)(DG)(DG)(DG)(DT)(DC)(DA)(DA)(DG)(DG)(DC) DNA 9-nt RNA transcript Escherichia coli O157:H7 0.002871767 1 GCAGUCUGA CHAPSO 0.000631884 2 1N7 MAGNESIUM ION 2.4305e-05 1 MG ZINC ION 6.5409e-05 2 ZN singleParticle particle 5 7.5 Quantifoil R1.2/1.3 GOLD 300 CARBON HOLEY GLOW DISCHARGE 15 AIR 101.325 ETHANE 100 295 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.2 2.2 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 1-44 13.2 50.46 1 372776

Ab-initio models were generated from a set of particles directly in cryoSPARC.

C1 2.8 FSC 0.143 CUT-OFF cryoSPARC 2.14 76916 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_22249.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 341.248 341.248 341.248 90.0 90.0 90.0 X Y Z -2.6534111 5.1639934 0.0024912786 0.1322163 1.333 1.333 1.333 0.67 AUTHOR ::::EMDATABANK.org::::EMD-22249:::: 6OUL PDB experimental model FLEXIBLE FIT Correlation coefficient REAL