2024-01-17 REL RCSB RCSB RCSB 2022-11-04 2023-04-05 2023-04-05 2024-01-17 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35 GM118130 United States EsN-dhsU36duplex full map (map 1) Mueller AU Chen J Darst SA promoter-bound, initiation, TRANSCRIPTION Mueller AU Chen J Wu M Chiu C Nixon BT Campbell EA Darst SA A general mechanism for transcription bubble nucleation in bacteria. Proc.Natl.Acad.Sci.USA US 120 e2220874120 e2220874120 2023 36972428 doi:10.1073/pnas.2220874120 1091-6490 0040 PNASA6 EMD-28790 other EM volume
local map
 EMD-28791 other EM volume
composite map
 EsN-dhsU36duplex EsN-dhsU36duplex 0 1 2 3 4 5 6 7 RNA polymerase alpha subunit Escherichia coli Escherichia coli LEVO MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILE ILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIH SEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLEN WPPASIADE P0A7Z4 RNA polymerase beta subunit Escherichia coli Escherichia coli LEVO MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVF DVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSD KGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQME LVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLD LLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAV GRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLS LGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCP IETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKG ESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKR GGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNM RVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGG DILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDL SEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGD DLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMA AKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLK LGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEA YGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE P0A8V2 RNA polymerase beta' subunit Escherichia coli Escherichia coli LEVO MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKH RGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQIL TEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILT VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSN KRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKM VEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDAN GELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVG IDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFN SIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRL VDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAV KVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKL SNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDM IDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDT LARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFE GERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQV EYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAG TGYAYHQDRMRRRAAGEAPAAPQVTAEDASASLAELLNAGLGGSDNELELEVLFQGPSSGHHHHHHHHHH P0A8T7 RNA polymerase omega subunit Escherichia coli Escherichia coli LEVO MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAELQAVTAIAEGRR P0A800 dhsU36duplex top strand Aquifex aeolicus (DC)(DC)(DA)(DG)(DA)(DA)(DA)(DT)(DT)(DG)(DG)(DC)(DA)(DC)(DG)(DA)(DA)(DA)(DA)(DT) (DT)(DG)(DC)(DA)(DA)(DT)(DA)(DA)(DA)(DT)(DA)(DC)(DA)(DA)(DC)(DG) DNA dhsU36duplex bottom strand Aquifex aeolicus (DC)(DG)(DT)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DA)(DT)(DT)(DG)(DC)(DA)(DA)(DT)(DT)(DT) (DT)(DC)(DG)(DT)(DG)(DC)(DC)(DA)(DA)(DT)(DT)(DT)(DC)(DT)(DG)(DG) DNA RNA polymerase sigma-54 factor Escherichia coli LEVO SEFMKQGLQLRLSQQLAMTPQLQQAIRLLQLSTLELQQELQQALESNPLLEQIDTHEEIDTRETQDSETLDTADALEQKE MPEELPLDASWDTIYTAGTPSGTSGDYIDDELPVYQGETTQTLQDYLMWQVELTPFSDTDRAIATSIVDAVDETGYLTVP LEDILESIGDEEIDIDEVEAVLKRIQRFDPVGVAAKDLRDCLLIQLSQFDKTTPWLEEARLIISDHLDLLANHDFRTLMR VTRLKEDVLKEAVNLIQSLDPRPGQSIQTGEPEYVIPDVLVRKHNGHWTVELNSDSIPRLQINQHYASMCNNARNDGDSQ FIRSNLQDAKWLIKSLESRNDTLLRVSRCIVEQQQAFFEQGEEYMKPMVLADIAQAVEMHESTISRVTTQKYLHSPRGIF ELKYFFSSHVNTEGGGEASSTAIRALVKKLIAAENPAKPLSDSKLTSLLSEQGIMVARRTVAKYRESLSIPPSNQRKQLV singleParticle particle 8.0 20.0 HEPES 100.0 KCH3COO potassium acetate 10.0 MgCl2 magnesium chloride 2.0 dithiothreitol C-flat-1.2/1.3 GOLD 400 CARBON HOLEY GLOW DISCHARGE AIR
Self-built glow discharge chamber was evacuated with a vacuum pump prior to application of voltage (no pressure and/or voltage readings available)
 ETHANE 100 295 FEI VITROBOT MARK IV
Octyl beta-D-glucopyranoside (beta-OG) was added to the sample to 0.1%w/v final concentration (from 10x stock) just prior to plunge vitrification.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.8 2.5 GIF Bioquantum 20 GATAN K3 (6k x 4k) 6088 2.0 51.32
dose-fractionation with 0.05 seconds per frame (=40 frames)
 1
ab initio generated map
 2.8 FSC 0.143 CUT-OFF cryoSPARC v3.2.0 NU refinement with global CTF and per-particle defocus refinement enabled 892568 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_28786.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 324 324 324 0 0 0 324 324 324 350.89197 350.89197 350.89197 90.0 90.0 90.0 X Y Z -0.6351043 1.9396987 0.0038927563 0.058458813 1.083 1.083 1.083 0.4 AUTHOR Raw map emd_28786_msk_1.map emd_28786_msk_2.map emd_28786_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 324 324 324 0 0 0 324 324 324 350.89197 350.89197 350.89197 90.0 90.0 90.0 X Y Z -8.548249 10.44068 0.0038927556 0.2011787 1.083 1.083 1.083 AUTHOR B-factor sharpened map (-121.3) emd_28786_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 324 324 324 0 0 0 324 324 324 350.89197 350.89197 350.89197 90.0 90.0 90.0 X Y Z -8.602081999999999 10.345753 0.0034003563 0.16763018 1.083 1.083 1.083 AUTHOR Locally filtered map (blocfilt) emd_28786_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 324 324 324 0 0 0 324 324 324 350.89197 350.89197 350.89197 90.0 90.0 90.0 X Y Z 0.0 45.566380000000002 0.16485679 0.8778795 1.083 1.083 1.083 AUTHOR Local resolution map (blocres) emd_28786_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 324 324 324 0 0 0 324 324 324 350.89197 350.89197 350.89197 90.0 90.0 90.0 X Y Z -0.62361604 2.006833 0.0037219925 0.06499026 1.083 1.083 1.083 AUTHOR Half map A emd_28786_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 324 324 324 0 0 0 324 324 324 350.89197 350.89197 350.89197 90.0 90.0 90.0 X Y Z -0.6512954 1.9844855 0.0037443845 0.0649962 1.083 1.083 1.083 AUTHOR Half map B