2024-05-15 REL RCSB RCSB RCSB 2019-06-13 2019-11-27 2020-03-18 2024-05-15 Liu B Shi W class-II, CAP-dependent, transcription activation complex, state 2 architecture, TRANSCRIPTION, TRANSCRIPTION-DNA complex Shi W Jiang Y Deng Y Dong Z Liu B Plos Biol. US 18 e3000706 2020 doi:10.1371/journal.pbio.3000706 1545-7885 EMD-20287 other EM volume

class-II CAP-dependent transcription activation complex at the state 1

EMD-20286 other EM volume

class-II CAP-dependent transcription activation complex with de novo RNA transcript at the state 2

6pb6 FULLOVERLAP The E. coli class-II CAP-dependent transcription activation complex at the state 2 The E. coli class-II CAP-dependent transcription activation complex at the state 2 0 1 2 3 4 5 6 7 8 Escherichia coli 0.55 DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', DNA-directed RNA polymerase subunit omega, RNA polymerase sigma factor RpoD, cAMP-activated global transcriptional regulator CRP 1 1 2 3 4 5 6 Escherichia coli DNA 1 7 8 DNA-directed RNA polymerase subunit alpha Escherichia coli 0.036558679999999996 2 Escherichia coli LEVO MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILE ILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIH SEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLEN WPPASIADE 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 B7MIX3 2.7.7.6 DNA-directed RNA polymerase subunit beta' Escherichia coli 0.15536678099999998 1 Escherichia coli 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 0.010249547 1 Escherichia coli LEVO MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAEL QAVTAIAEGRR B7MFL0 2.7.7.6 RNA polymerase sigma factor RpoD Escherichia coli 0.072206266 1 Escherichia coli LEVO MRGSHHHHHHTDQFTMEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL MLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLL EQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELR AQYVVTRDTIKAKGRSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITL FTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLR LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNR ISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATH DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD P00579 cAMP-activated global transcriptional regulator CRP Escherichia coli 0.023672438999999997 2 Escherichia coli LEVO MVLGKPQTDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEG QERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTH PDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGTR P0ACK0 SYNTHETIC NONTEMPLATE STRAND DNA (78-MER) Escherichia coli 0.023976331999999996 1 (DC)(DT)(DT)(DT)(DT)(DT)(DT)(DG)(DC)(DC)(DT)(DA)(DA)(DA)(DA)(DT)(DG)(DT)(DG)(DA) (DT)(DC)(DT)(DA)(DG)(DA)(DT)(DC)(DA)(DC)(DA)(DT)(DT)(DT)(DT)(DT)(DC)(DG)(DC)(DA) (DT)(DC)(DT)(DT)(DT)(DT)(DT)(DT)(DA)(DT)(DG)(DC)(DT)(DA)(DT)(DA)(DA)(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 (78-MER) Escherichia coli 0.02419159 1 (DC)(DG)(DC)(DC)(DG)(DC)(DG)(DT)(DC)(DA)(DG)(DA)(DC)(DT)(DC)(DG)(DT)(DA)(DG)(DG) (DA)(DT)(DT)(DA)(DT)(DA)(DG)(DC)(DA)(DT)(DA)(DA)(DA)(DA)(DA)(DA)(DG)(DA)(DT)(DG) (DC)(DG)(DA)(DA)(DA)(DA)(DA)(DT)(DG)(DT)(DG)(DA)(DT)(DC)(DT)(DA)(DG)(DA)(DT)(DC) (DA)(DC)(DA)(DT)(DT)(DT)(DT)(DA)(DG)(DG)(DC)(DA)(DA)(DA)(DA)(DA)(DA)(DG) DNA ZINC ION 6.5409e-05 2 ZN MAGNESIUM ION 2.4305e-05 1 MG ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE 0.000329206 2 CMP singleParticle particle 0.55 7.5 20.0 Tris 2-Amino-2-hydroxymethyl-1,3-propanediol 50.0 NaCl sodium chloride 5.0 MgCl2 magnesium chloride Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY 120.0 GLOW DISCHARGE 60 AIR

15 mA

ETHANE 100 277 FEI VITROBOT MARK IV

blot for 3 seconds before plunging.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 0.8 2.6 96000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 77.0 77.0

Direct alignments: Beam tilt pivot points, Beam shift, Comma Free. C2 aperture centering, C2 lens astigmatism correction. Objective aperture centering and objective lens astigmatism correction.

FEI FALCON III (4k x 4k) COUNTING 45.0 45.0 1 4.29 FSC 0.143 CUT-OFF cisTEM 37456 NOT APPLICABLE NOT APPLICABLE