2024-03-27 REL PDBj PDBj PDBj 2019-11-21 2020-09-30 2020-09-30 2024-03-27 National Natural Science Foundation of China 31822001 China The cryo-EM structure of E. coli CueR transcription activation complex Fang CL Zhang Y RNA polymerase, CueR, transcription activation, TRANSCRIPTION, TRANSCRIPTION (DNA to RNA) Fang C Philips SJ Wu X Chen K Shi J Shen L Xu J Feng Y O'Halloran TV Zhang Y CueR activates transcription through a DNA distortion mechanism. Nat.Chem.Biol. US 17 57 64 2021 32989300 doi:10.1038/s41589-020-00653-x 1552-4469 6ldi FULLOVERLAP Escherichia coli CueR transcription activation complex Escherichia coli CueR transcription activation complex 0 1 2 3 4 5 6 7 8 9 Escherichia coli K-12 0.507 DNA-directed RNA polymerase subunit alpha Escherichia coli (strain K12) K12 0.036558679999999996 2 Escherichia coli LEVO MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILE ILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIH SEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLEN WPPASIADE P0A7Z4 2.7.7.6 DNA-directed RNA polymerase subunit beta Escherichia coli (strain K12) K12 0.150820875 1 Escherichia coli 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) K12 0.156537031 1 Escherichia coli LEVO MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKH RGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQIL TEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILT VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSN KRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKM VEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDAN GELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVG IDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFN SIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRL VDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAV KVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKL SNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDM IDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDT LARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFE GERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQV EYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAG TGYAYHQDRMRRRAAGEAPAAPQVTAEDASASLAELLNAGLGGSDNELEVHHHHHH P0A8T7 2.7.7.6 DNA-directed RNA polymerase subunit omega Escherichia coli (strain K12) K12 0.010249547 1 Escherichia coli LEVO MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAEL QAVTAIAEGRR P0A800 2.7.7.6 RNA polymerase sigma factor RpoD Escherichia coli (strain K12) K12 0.072523633 1 Escherichia coli LEVO MGSSHHHHHHSSGLVPRGSHMEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAP DADDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEA ITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREK FAELRAQYVVTRDTIKAKGRSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKK NFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMV EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI NKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESL RAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD P00579 DNA (50-MER) synthetic construct 0.015415855 1 (DC)(DT)(DT)(DG)(DA)(DC)(DC)(DT)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DC)(DT)(DG)(DG) (DA)(DA)(DG)(DG)(DT)(DT)(DT)(DA)(DT)(DA)(DA)(DT)(DG)(DG)(DG)(DA)(DG)(DC)(DT)(DG) (DT)(DC)(DA)(DC)(DG)(DG)(DA)(DT)(DG)(DC) DNA DNA (50-MER) synthetic construct 0.015559003 1 (DG)(DC)(DA)(DT)(DC)(DC)(DG)(DT)(DG)(DA)(DG)(DT)(DC)(DG)(DA)(DG)(DG)(DG)(DT)(DA) (DA)(DT)(DA)(DA)(DA)(DA)(DC)(DC)(DT)(DT)(DC)(DC)(DA)(DG)(DC)(DA)(DA)(DG)(DG)(DG) (DG)(DA)(DA)(DG)(DG)(DT)(DC)(DA)(DA)(DG) DNA RNA (5'-R(*CP*UP*CP*GP*A)-3') synthetic construct 0.0015459839999999998 1 CUCGA HTH-type transcriptional regulator CueR Escherichia coli (strain K12) K12 0.01558657 2 Escherichia coli LEVO GAMAMNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRH SADVKRRTLEKVAEIERHIEELQSMRDQLLALANACPGDDSADCPIIENLSGCCHHRAG P0A9G4 ZINC ION 6.5409e-05 2 ZN MAGNESIUM ION 2.4305e-05 1 MG SILVER ION 0.00010786799999999999 1 AG singleParticle particle 15 8.0 10.0 C8H18N2O4S HEPES 50.0 KCl Potassium Chloride 5.0 MgCl2 Magnesium chloride 3.0 C4H10O2S2 DL-Dithiothreitol C-flat-1.2/1.3 4C COPPER 400 CARBON HOLEY 120.0 GLOW DISCHARGE OTHER ETHANE 95 282.65 FEI VITROBOT MARK III FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 GATAN K2 SUMMIT (4k x 4k) COUNTING 1 2278 12.0 56.0 1 617318 EMD-9792 1 C1 FOURIER SPACE 3.69 FSC 0.143 CUT-OFF RELION 3.0 184524 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0 4 RELION 3.0 emd_0874.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 392.1 392.1 392.1 90.0 90.0 90.0 X Y Z -0.06349809 0.12396796 0.00017569494 0.0027082074 1.307 1.307 1.307 0.02 AUTHOR 6B6H PDB experimental model 4WLS PDB experimental model RIGID BODY FIT emd_0874_msk_1.map emd_0874_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 392.1 392.1 392.1 90.0 90.0 90.0 X Y Z -0.031281367 0.06991363 0.00000974011 0.0031245793 1.307 1.307 1.307 AUTHOR emd_0874_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 392.1 392.1 392.1 90.0 90.0 90.0 X Y Z -0.06349809 0.12396796 0.00017569494 0.0027082074 1.307 1.307 1.307 AUTHOR