RNA polymerase- post-terminated, open clamp state

Structural insights into RNA-mediated transcription regulation in bacteria.

20 mM Tris-glutamate pH 8.0, 50 mM K-glutamate, 10 mM Mg-glutamate, 0.001 mM ZnCl2, 2mM DTT

Escherichia coli RNA polymerase post-terminated complex - open clamp state

The co-transcriptionally halted complexes for cryo-EM analysis were prepared in vitro by mixing E. coli RNAP holoenzyme with templates containing the DNA base analogue isoG. The RNAP ECs halted at the U-rich pause (G122). The complexes were prepared in 0.03 ml reactions and contained: 0.02 mM of E. coli RNAP, 0.080 mM of E. coli Sigma70, 0.02 mM of template DNA, 20 mM Tris-glutamate pH 8.0, 50 mM K-glutamate, 10 mM Mg-glutamate, 0.001 mM ZnCl2, 2mM DTT and 6 mM of each ATP, GTP, CTP and UTP. Initially, all the components except NTPs were added and incubated for 10 min at 310K. To allow transcription elongation, NTPs were added and the sample was incubated for 20 to 40 min at 310K. The final products were purified on a Superose 6 Increase 3.2/300 gel filtration column equilibrated in Glutamate buffer. Samples were concentrated to 10-12 mg/mL using an Amicon Ultra 0.5mL centrifugal filter unit (30 KDa MWCO). Before grid freezing, 8 mM of CHAPSO was added to freshly prepared sample to overcome preferred particle orientation.

Quantifoil UltrAuFoil R1.2/1.3 300 mesh holey gold grids were plasma cleaned on a Model 1070 (Fischione Instruments) for 30 sec at 70% power and with an 80% Argon and 20% Oxygen mixture prior to the application of 0.004 ml of sample. Grids were plunge frozen into liquid ethane using a Vitrobot mark IV (FEI) with 95% chamber humidity at 283K.

DNA-directed RNA polymerase subunit alpha

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit beta'

DNA-directed RNA polymerase subunit omega

RNAP subunit alpha,RNA polymerase subunit alpha,Transcriptase subunit alpha

RNAP subunit beta,RNA polymerase subunit beta,Transcriptase subunit beta

RNAP subunit beta',RNA polymerase subunit beta',Transcriptase subunit beta'

RNAP omega subunit,RNA polymerase omega subunit,Transcriptase subunit omega

MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILE
ILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIH
SEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP
EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLEN
WPPASIADE

MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVF
DVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSD
KGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQME
LVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLD
LLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAV
GRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLS
LGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCP
IETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKG
ESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKR
GGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNM
RVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGG
DILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDL
SEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGD
DLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMA
AKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLK
LGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEA
YGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE

MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKH
RGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQIL
TEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILT
VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSN
KRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKM
VEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA
RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDAN
GELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVG
IDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFN
SIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRL
VDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAV
KVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKL
SNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDM
IDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDT
LARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFE
GERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQV
EYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAG
TGYAYHQDRMRRRAAGEAPAAPQVTAEDASASLAELLNAGLGGSDN

MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAEL
QAVTAIAEGRR

(DC)(DA)(DG)(DT)(DC)(DA)(DC)(DG)(DA)(DC)(DG)(DT)(DT)(DG)(DT)(DA)(DA)(DA)(DA)(DC)
(DG)(DA)(DC)(DG)(DG)(DC)(DC)(DA)(DG)(DT)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DA)(DG)(DC)
(DT)(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DA)(DA)(DA)(DA)(DA)(DT)(DA)(DA)(DA)(DT)(DT)(DT)
(DC)(DC)(DT)(DT)(DA)(DA)(DA)(DG)(DT)(DT)(DC)(DA)(DC)(DT)(DA)(DA)(DC)(DT)(DT)(DA)
(DT)(DG)(DA)(DT)(DG)(DT)(DA)(DG)(DT)(DG)(DA)(DG)(DC)(DT)(DT)(DT)(DT)(DT)(DA)(DT)
(DA)(DC)(DC)(DC)(DA)(DT)(DA)(DA)(DA)(DA)(DT)(DG)(DT)(DA)(DC)(DT)(DA)(DT)(DT)(DG)
(DG)(DT)(DA)(DC)(DT)(DT)(DT)(DA)(DC)(DA)(DT)(DT)(DA)(DA)(DT)(DG)(DA)(DA)(DC)(DT)
(DT)(DT)(DA)(DA)(DG)(DT)(DA)(DC)(DA)(DT)(DC)(DA)(DT)(DA)(DA)(DG)(DC)(DC)(DC)(DA)
(DT)(DC)(DG)(DA)(DG)(DA)(DG)(DG)(DG)(DA)(DC)(DA)(DC)(DG)(DG)(DG)(DG)(DA)(DA)(DA)
(DC)(DA)(DC)(DC)(DA)(DC)(DC)(DA)(DT)(DG)(DC)(DT)(DT)(DA)(DT)(DA)(DA)(DT)(DA)(DA)
(DT)(DT)(DC)(DT)(DG)(DC)(DC)(DG)(DG)(DA)(DG)(DC)(DG)(DA)(DC)(DC)(DG)(DC)(DA)(DC)
(DT)(DG)(DT)(DG)(DG)(DT)(DT)(DT)(DA)(DC)(DC)(DA)(DG)(DA)(DT)(DG)(DG)(DC)(DG)(DT)
(DG)(DT)(DG)(DT)(DC)(DC)(DC)(DA)(DA)(DT)(DC)(DT)(DT)(DT)(DC)(DA)(DC)(DA)(DA)(DC)
(DA)(DT)(DT)(DA)(DG)(DC)(DG)(DA)(DG)(DA)(DA)(DG)(DG)(DC)(DT)(DT)(DT)(DT)(DT)(DT)
(DG)(DT)(DT)(DT)(DT)(DT)(DA)(DG)(DT)(DC)(DA)(DC)(DG)(DG)(DC)

CAGTCACGACGTTGTAAAACGACGGCCAGTGAATTCGAGCTCGGTACCAAAAATAAATTTCCTTAAAGTTCACTAACTTA
TGATGTAGTGAGCTTTTTATACCCATAAAATGTACTATTGGTACTTTACATTAATGAACTTTAAGTACATCATAAGCCCA
TCGAGAGGGACACGGGGAAACACCACCATGCTTATAATAATTCTGCCGGAGCGACCGCACTGTGGTTTACCAGATGGCGT
GTGTCCCAATCTTTCACAACATTAGCGAGAAGGCTTTTTTGTTTTTAGTCACGGC

(DG)(DC)(DC)(DG)(DT)(DG)(DA)(DC)(DT)(DA)(DA)(DA)(IGU)(IGU)(DC)(DA)(DA)(DA)(DA)
(DA)(DA)(DG)(DC)(DC)(DT)(DT)(DC)(DT)(DC)(DG)(DC)(DT)(DA)(DA)(DT)(DG)(DT)(DT)(DG)
(DT)(DG)(DA)(DA)(DA)(DG)(DA)(DT)(DT)(DG)(DG)(DG)(DA)(DC)(DA)(DC)(DA)(DC)(DG)(DC)
(DC)(DA)(DT)(DC)(DT)(DG)(DG)(DT)(DA)(DA)(DA)(DC)(DC)(DA)(DC)(DA)(DG)(DT)(DG)(DC)
(DG)(DG)(DT)(DC)(DG)(DC)(DT)(DC)(DC)(DG)(DG)(DC)(DA)(DG)(DA)(DA)(DT)(DT)(DA)(DT)
(DT)(DA)(DT)(DA)(DA)(DG)(DC)(DA)(DT)(DG)(DG)(DT)(DG)(DG)(DT)(DG)(DT)(DT)(DT)(DC)
(DC)(DC)(DC)(DG)(DT)(DG)(DT)(DC)(DC)(DC)(DT)(DC)(DT)(DC)(DG)(DA)(DT)(DG)(DG)(DG)
(DC)(DT)(DT)(DA)(DT)(DG)(DA)(DT)(DG)(DT)(DA)(DC)(DT)(DT)(DA)(DA)(DA)(DG)(DT)(DT)
(DC)(DA)(DT)(DT)(DA)(DA)(DT)(DG)(DT)(DA)(DA)(DA)(DG)(DT)(DA)(DC)(DC)(DA)(DA)(DT)
(DA)(DG)(DT)(DA)(DC)(DA)(DT)(DT)(DT)(DT)(DA)(DT)(DG)(DG)(DG)(DT)(DA)(DT)(DA)(DA)
(DA)(DA)(DA)(DG)(DC)(DT)(DC)(DA)(DC)(DT)(DA)(DC)(DA)(DT)(DC)(DA)(DT)(DA)(DA)(DG)
(DT)(DT)(DA)(DG)(DT)(DG)(DA)(DA)(DC)(DT)(DT)(DT)(DA)(DA)(DG)(DG)(DA)(DA)(DA)(DT)
(DT)(DT)(DA)(DT)(DT)(DT)(DT)(DT)(DG)(DG)(DT)(DA)(DC)(DC)(DG)(DA)(DG)(DC)(DT)(DC)
(DG)(DA)(DA)(DT)(DT)(DC)(DA)(DC)(DT)(DG)(DG)(DC)(DC)(DG)(DT)(DC)(DG)(DT)(DT)(DT)
(DT)(DA)(DC)(DA)(DA)(DC)(DG)(DT)(DC)(DG)(DT)(DG)(DA)(DC)(DT)(DG)

GCCGTGACTAAAGGCAAAAAAGCCTTCTCGCTAATGTTGTGAAAGATTGGGACACACGCCATCTGGTAAACCACAGTGCG
GTCGCTCCGGCAGAATTATTATAAGCATGGTGGTGTTTCCCCGTGTCCCTCTCGATGGGCTTATGATGTACTTAAAGTTC
ATTAATGTAAAGTACCAATAGTACATTTTATGGGTATAAAAAGCTCACTACATCATAAGTTAGTGAACTTTAAGGAAATT
TATTTTTGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTG

rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950
French Infrastructure for Integrated Structural Biology (FRISBI)
RNA polymerase, transcriptional pausing, transcription termination, regulatory RNA, TRANSCRIPTION