Cryo-EM structure of bacterial RNAP with a DNA mimic protein Ocr from T7 phage

2024-11-06 REL PDBe PDBe PDBe 2019-04-03 2018-06-06 2020-02-26 2024-11-06 Biotechnology and Biological Sciences Research Council (BBSRC) BB/N007816 United Kingdom Cryo-EM structure of bacterial RNAP with a DNA mimic protein Ocr from T7 phage Ye FZ Zhang XD TRANSCRIPTION, RNA polymerase, Ocr, transcription inhibition, bacteriophage T7 Ye F Kotta-Loizou I Jovanovic M Liu X Dryden DT Buck M Zhang X Structural basis of transcription inhibition by the DNA mimic protein Ocr of bacteriophage T7. Elife US 9 2020 32039758 doi:10.7554/eLife.52125 2050-084X 6r9b FULLOVERLAP Structural basis of transcription inhibition by the DNA mimic Ocr protein of bacteriophage T7 Structural basis of transcription inhibition by the DNA mimic Ocr protein of bacteriophage T7 0 1 2 3 4 5 0.410 DNA-directed RNA polymerase 1 1 2 3 4 Escherichia coli K-12 Ocr (Overcome classical restriction) 1 5 Enterobacteria phage T7 DNA-directed RNA polymerase subunit alpha Escherichia coli (strain K12) K12 0.036558679999999996 2 Escherichia coli BL21(DE3) 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 BL21(DE3) 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 0.15536678099999998 1 Escherichia coli BL21(DE3) 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 K-12 0.009094238999999999 1 Escherichia coli BL21(DE3) LEVO MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAEL F4NQ47 2.7.7.6 Overcome classical restriction gp0.3 Enterobacteria phage T7 0.013819014999999999 2 Escherichia coli BL21(DE3) LEVO MAMSNMTYNNVFDHAYEMLKENIRYDDIRDTDDLHDAIHMAADNAVPHYYADIFSVMASEGIDLEFEDSGLMPDTKDVIR ILQARIYEQLTIDLWEDAEDLLNEYLEEVEEYEEDEE P03775 singleParticle particle 0.6 8.0 20.0 Tris-HCL Tris hydrochloride 150.0 NaCL sodium chloride 5.0 MgCl2 magnesium chloride 1.0 TCEP TCEP Quantifoil R2/2 200 PLASMA CLEANING 30 ETHANE 95 277 FEI VITROBOT MARK IV FEI TITAN KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 -0.0012 -0.003 GATAN K2 SUMMIT (4k x 4k) COUNTING 1 3543 1.0 49.53 1 753783 6GH5 1 C1 3.8 FSC 0.143 CUT-OFF 27312 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_4769.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 270.08 270.08 270.08 90.0 90.0 90.0 X Y Z -0.1476005 0.22251263 -0.0000626079 0.005031045 1.055 1.055 1.055 0.004 AUTHOR ::::EMDATABANK.org::::EMD-4769:::: None RIGID BODY FIT REAL