2025-05-28 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name STRUCTURE_SUMMARY em_admin pdbx_entry_details pdbx_modification_feature _em_admin.last_update _pdbx_entry_details.has_protein_modification DATABASE_REFERENCES citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID _em_admin.last_update DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name RCSB RCSB 2023-08-03 2024-07-03 2024-07-03 2025-05-28 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35 GM118130 United States Darst SA Saecker RM Mueller AU DNA-dependent RNA polymerase, transcription, intermediate, DNA promoter, DNA unwinding, transcription-DNA complex Saecker RM Mueller AU Malone B Chen J Budell WC Dandey VP Maruthi K Mendez JH Molina N Eng ET Yen LY Potter CS Carragher B Darst SA Nat.Struct.Mol.Biol. US 31 1778 1788 2024 38951624 doi:10.1038/s41594-024-01349-9 1545-9985 Darst SA Saecker RM Mueller AU Malone B Chen J Budell WC Dandey VP Maruthi K Mendez JH Molina N Eng ET Yen LY Potter CS Carragher B Nat.Struct.Mol.Biol. US 2024 doi:0.1038/s41594-024-01349-9 1545-9985 8tom FULLOVERLAP Escherichia coli RNA polymerase closed complex intermediate at the lambda PR promoter Escherichia coli RNA polymerase closed complex intermediate at the lambda PR promoter 0 1 2 3 4 5 6 7 Escherichia coli DNA-directed RNA polymerase subunit alpha Escherichia coli (strain K12) 0.036558679999999996 3 Escherichia coli 'BL21-Gold(DE3)pLysS AG' LEVO MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILE ILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIH SEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLEN WPPASIADE P0A7Z4 2.7.7.6 DNA-directed RNA polymerase subunit beta Escherichia coli (strain K12) 0.150820875 1 Escherichia coli 'BL21-Gold(DE3)pLysS AG' 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 (strain K12) 0.15536678099999998 1 Escherichia coli 'BL21-Gold(DE3)pLysS AG' LEVO MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKH RGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQIL TEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILT VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSN KRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKM VEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDAN GELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVG IDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFN SIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRL VDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAV KVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKL SNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDM IDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDT LARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFE GERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQV EYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAG TGYAYHQDRMRRRAAGEAPAAPQVTAEDASASLAELLNAGLGGSDNE P0A8T7 2.7.7.6 DNA-directed RNA polymerase subunit omega Escherichia coli (strain K12) 0.010249547 1 Escherichia coli 'BL21-Gold(DE3)pLysS AG' LEVO MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAEL QAVTAIAEGRR P0A800 2.7.7.6 RNA polymerase sigma factor RpoD Escherichia coli (strain K12) 0.070352242 1 Escherichia coli 'BL21-Gold(DE3)pLysS AG' LEVO MEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAENTADEDAAEAA AQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSD LITGFVDPNAEEDLAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGR SHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAI AMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQ FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLR MRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD Q0P6L9 Nontemplate strand of lamdba PR promoter DNA Escherichia phage Lambda 0.027881813999999998 1 (DG)(DG)(DA)(DT)(DA)(DA)(DA)(DT)(DA)(DT)(DC)(DT)(DA)(DA)(DC)(DA)(DC)(DC)(DG)(DT) (DG)(DC)(DG)(DT)(DG)(DT)(DT)(DG)(DA)(DC)(DT)(DA)(DT)(DT)(DT)(DT)(DA)(DC)(DC)(DT) (DC)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DG)(DA)(DT)(DA)(DA)(DT)(DG)(DG)(DT)(DT)(DG)(DC) (DA)(DT)(DG)(DT)(DA)(DC)(DT)(DA)(DA)(DG)(DG)(DA)(DG)(DG)(DT)(DT)(DG)(DT)(DA)(DT) (DG)(DT)(DC)(DG)(DA)(DC)(DC)(DT)(DC)(DG) DNA Template strand of lamdba PR promoter DNA Escherichia phage Lambda 0.02763374 1 (DC)(DG)(DA)(DG)(DG)(DT)(DC)(DG)(DA)(DC)(DA)(DT)(DA)(DC)(DA)(DA)(DC)(DC)(DT)(DC) (DC)(DT)(DT)(DA)(DG)(DT)(DA)(DC)(DA)(DT)(DG)(DC)(DA)(DA)(DC)(DC)(DA)(DT)(DT)(DA) (DT)(DC)(DA)(DC)(DC)(DG)(DC)(DC)(DA)(DG)(DA)(DG)(DG)(DT)(DA)(DA)(DA)(DA)(DT)(DA) (DG)(DT)(DC)(DA)(DA)(DC)(DA)(DC)(DG)(DC)(DA)(DC)(DG)(DG)(DT)(DG)(DT)(DT)(DA)(DG) (DA)(DT)(DA)(DT)(DT)(DT)(DA)(DT)(DC)(DC) DNA CHAPSO 0.000631884 4 1N7 MAGNESIUM ION 2.4305e-05 1 MG ZINC ION 6.5409e-05 2 ZN singleParticle particle 8.0 40.0 Tris 120.0 KCl potassium chloride 10.0 MgCl2 magnesium chloride 10.0 DTT 1,4-dithiothreitol C-flat-1.2/1.3 GOLD 400 CARBON HOLEY PLASMA CLEANING 20 AIR ETHANE 100 278.2 FEI VITROBOT MARK IV

CHAPSO was added (from 80 mM stock) to 8 mM final..

Es70 RNAP 15 micromolar, LPR DNA 18 micromolar

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 2.5 GIF Bioquantum 20 GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 60.0 1 581275 cryoSPARC 3.2.0 Patch CTF PHASE FLIPPING AND AMPLITUDE CORRECTION

Ab initio generated map

3.1 FSC 0.143 CUT-OFF cryoSPARC 3.2.0 NU refinement 122806 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD cryoSPARC 3.2.0 3DVA emd_41456_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 422.40002 422.40002 422.40002 90.0 90.0 90.0 X Y Z -0.787411 2.3100011 0.001583779 0.053439308 1.1 1.1 1.1 AUTHOR ::::EMDATABANK.org::::EMD-41456:::: EcRNAP-LPR promoter closed complex unsharpened map emd_41456_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 422.40002 422.40002 422.40002 90.0 90.0 90.0 X Y Z -3.727176 5.213831 0.0015837791 0.10198024 1.1 1.1 1.1 AUTHOR ::::EMDATABANK.org::::EMD-41456:::: Additional Map 2 emd_41456_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 422.40002 422.40002 422.40002 90.0 90.0 90.0 X Y Z -1.026348 2.5877378 0.0027782067 0.09992773 1.1 1.1 1.1 AUTHOR ::::EMDATABANK.org::::EMD-41456:::: EcRNAP-LPR promoter closed complex half map B emd_41456_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 422.40002 422.40002 422.40002 90.0 90.0 90.0 X Y Z -1.0287142 2.6203516 0.0027785988 0.09981601 1.1 1.1 1.1 AUTHOR ::::EMDATABANK.org::::EMD-41456:::: EcRNAP-LPR promoter closed complex half map A