2024-05-29 REL RCSB RCSB RCSB 2023-05-24 2023-12-27 2023-12-27 2024-05-29 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM102362 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM148476 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) U54 AI170855 United States National Science Foundation (NSF, United States) MCB-2048095 United States National Institutes of Health/National Cancer Institute (NIH/NCI) 1R21CA251043-01A1 United States National Science Foundation (NSF, United States) MCB- 2123995 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) U24 GM129541 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) S10 OD032467 United States E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dB-UTP base pair in the active site Shan Z Lyumkis D Oh J Wang D complex, unnatural base pairs, synthetic biology, transcription, TRANSCRIPTION-DNA-RNA complex Oh J Shan Z Hoshika S Xu J Chong J Benner SA Lyumkis D Wang D A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase. Nat Commun UK 14 8219 8219 2023 38086811 doi:10.1038/s41467-023-43735-9 2041-1723 8sy6 FULLOVERLAP E. coli RNAP transcription elongation complex bound the unnatural dB-UTP base pair in the active site E. coli RNAP transcription elongation complex bound the unnatural dB-UTP base pair in the active site 0 1 2 3 4 5 6 7 Escherichia coli 0.5 Non-template single stranded DNA synthetic construct 0.005663694 1 (DT)(DC)(DA)(DG)(DC)(DG)(DA)(DG)(DA)(DG)(DA)(DG)(DA)(DG)(DA)(DA)(DG)(DG) DNA Template single stranded DNA synthetic construct 0.008739593999999998 1 (DC)(DC)(DT)(DT)(DC)(DT)(DC)(DT)(DC)(DT)(DC)(DT)(DC)(DG)(DC)(DT)(DG)(DA)(IGU) (DC)(DC)(DT)(DC)(DT)(DC)(DG)(DA)(DT)(DG) DNA DNA-directed RNA polymerase subunit alpha Escherichia coli 0.036558679999999996 2 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 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 0.15810567199999997 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 TGYAYHQDRMRRRAAGEAPAAPQVTAEDASASLAELLNAGLGGSDNELELEVLFQGPSSGHHHHHHHHHH P0A8T7 2.7.7.6 RNA oligomer synthetic construct 0.002934831 1 AUCGAGAGG DNA-directed RNA polymerase subunit omega Escherichia coli 0.010249547 1 Escherichia coli 'BL21-Gold(DE3)pLysS AG' LEVO MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAEL QAVTAIAEGRR P0A800 2.7.7.6 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE 0.000347221 1 DGP ZINC ION 6.5409e-05 2 ZN MAGNESIUM ION 2.4305e-05 1 MG URIDINE 5'-TRIPHOSPHATE 0.000484141 1 UTP singleParticle particle 15 8.0
20mM Tris (pH 8.0), 40mM KCl, 5mM DTT and 5mM MgCl2
 UltrAuFoil R1.2/1.3 GOLD 300 GOLD HOLEY PLASMA CLEANING ETHANE 90
The sample was concentrated to 15mg/ml with 4 mM CHAPSO
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 1.0 2.5 60240.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K2 QUANTUM (4k x 4k) 5300 33.8 1 544816 C1 3.28 FSC 0.143 CUT-OFF cryoSPARC 4.2.1 268973 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_40863.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 265.6 265.6 265.6 90.0 90.0 90.0 X Y Z -0.109252766 0.51339656 0.0114845 0.03218271 0.83000004 0.83000004 0.83000004 0.18 AUTHOR The full map of E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dB-UTP base pair in the active site Other experimental model
Used dB-STP atomic model
 FLEXIBLE FIT REAL emd_40863_msk_1.map emd_40863_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 265.6 265.6 265.6 90.0 90.0 90.0 Z Y X -1.4482332 2.1508112 -0.000005257722 0.06049824 0.83000004 0.83000004 0.83000004 AUTHOR The density modified map of E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dB-UTP base pair in the active site that used for atomic modeling emd_40863_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 265.6 265.6 265.6 90.0 90.0 90.0 X Y Z -0.59139794 0.60924345 0.007980275 0.07218288 0.83000004 0.83000004 0.83000004 AUTHOR The half map2 of E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dB-UTP base pair in the active site emd_40863_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 265.6 265.6 265.6 90.0 90.0 90.0 X Y Z -0.63696337 0.62698495 0.008032159 0.07210716 0.83000004 0.83000004 0.83000004 AUTHOR The half map1 of E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dB-UTP base pair in the active site