2024-06-19 REL RCSB RCSB RCSB 2022-09-13 2023-03-01 2023-03-01 2024-06-19 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM118130 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM38330 United States Cryo-EM structure of his-elemental paused elongation complex with a folded TL and a rotated RH-FL (1) Kang JY Chen J Llewellyn E Landick R Darst SA RNA polymerase, cryo-EM structure, elemental pause, Escherichia coli, transcription, TRANSFERASE-DNA-RNA complex, transcriptional regulation, transcriptional pausing Kang JY Mishanina TV Bao Y Chen J Llewellyn E Liu J Darst SA Landick R An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options. Proc.Natl.Acad.Sci.USA US 120 e2215945120 e2215945120 2023 36795753 doi:10.1073/pnas.2215945120 1091-6490 0040 PNASA6 EMD-28109 other EM volume EMD-28110 other EM volume EMD-28113 other EM volume EMD-28144 other EM volume EMD-28145 other EM volume 8eh8 FULLOVERLAP his-elemental paused elongation complex his-elemental paused elongation complex 0 1 2 3 4 5 6 7
An RNA polymerase elongation complex was assembled at the weak elemental pausing site derived from his-pause sequence.
Escherichia coli 0.45 non-template DNA Escherichia coli 0.009881363999999998 1 (DG)(DC)(DG)(DT)(DC)(DC)(DT)(DA)(DT)(DC)(DG)(DA)(DT)(DC)(DT)(DT)(DC)(DG)(DG)(DA) (DA)(DG)(DA)(DG)(DA)(DT)(DT)(DC)(DA)(DG)(DA)(DG) DNA template DNA Escherichia coli 0.009706255999999998 1 (DC)(DT)(DC)(DT)(DG)(DA)(DA)(DT)(DC)(DT)(DC)(DT)(DT)(DC)(DC)(DA)(DG)(DC)(DA)(DC) (DA)(DC)(DA)(DT)(DC)(DA)(DG)(DG)(DA)(DC)(DG)(DC) DNA RNA Escherichia coli 0.0060475929999999995 1 UCAUCCGGCGAUGUGUGCU DNA-directed RNA polymerase subunit alpha Escherichia coli 0.026459125 2 Escherichia coli LEVO MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILE ILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIH SEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLEVLFQ P0A7Z6 2.7.7.6 DNA-directed RNA polymerase subunit beta Escherichia coli 0.150820875 1 Escherichia coli LEVO MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVF DVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSD KGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQME LVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLD LLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAV GRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLS LGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCP IETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKG ESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKR GGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNM RVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGG DILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDL SEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGD DLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMA AKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLK LGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEA YGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE P0A8V4 2.7.7.6 DNA-directed RNA polymerase subunit beta' Escherichia coli 0.155334719 1 Escherichia coli LEVO VKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKH RGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQIL TEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILT VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSN KRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKM VEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDAN GELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVG IDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFN SIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRL VDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAV KVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKL SNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDM IDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDT LARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFE GERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQV EYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAG TGYAYHQDRMRRRAAGEAPAAPQVTAEDASASLAELLNAGLGGSDNE C3SIA2 2.7.7.6 DNA-directed RNA polymerase subunit omega Escherichia coli 0.010249547 1 Escherichia coli LEVO MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAEL QAVTAIAEGRR P0A802 2.7.7.6 MAGNESIUM ION 2.4305e-05 1 MG CHAPSO 0.000631884 1 1N7 ZINC ION 6.5409e-05 2 ZN singleParticle particle 7 8.0 20.0 Tris 150.0 potassium glutamate 5.0 MgCl2 magnesium chloride 5.0 dithiothreitol C-flat-1.2/1.3 GOLD CARBON HOLEY PLASMA CLEANING AIR ETHANE 100 295 FEI VITROBOT MARK IV
blot force 0, blot time 3.5 s.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.8 2.4 FEI TITAN KRIOS AUTOGRID HOLDER GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 3710 3838 1-50 1 6939 10.0 47.34 1 2126200
Ab initio map was reconstructed in Cryosparc2 using the picked particles.
 1 C1 BACK PROJECTION 3.4 FSC 0.143 CUT-OFF RELION 150900 ANGULAR RECONSTITUTION cryoSPARC 2 ANGULAR RECONSTITUTION RELION 3 79400.0 RELION emd_28143.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 332.8 332.8 332.8 90.0 90.0 90.0 X Y Z -0.14711776 0.2152721 0.000016564054 0.0069524753 1.3 1.3 1.3 0.028 AUTHOR a postprocessed map 6C6T G 7-234 PDB experimental model 6C6T H 4-232 PDB experimental model 6C6T I 2-1342 PDB experimental model 6C6T J 16-1373 PDB experimental model 6C6T K 2-84 PDB experimental model RIGID BODY FIT REAL emd_28143_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 332.8 332.8 332.8 90.0 90.0 90.0 X Y Z -0.03427488 0.08487985 0.000025291634 0.0034944445 1.3 1.3 1.3 AUTHOR a first half-map emd_28143_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 332.8 332.8 332.8 90.0 90.0 90.0 X Y Z -0.034494147 0.07983358 0.000007836475 0.0034935055 1.3 1.3 1.3 AUTHOR a second half-map