Cryo-EM structure of Bacillus subtilis RNA Polymerase elongation complex

2024-05-29 REL RCSB RCSB RCSB 2020-05-06 2020-11-18 2020-11-18 2024-05-29 Cryo-EM structure of Bacillus subtilis RNA Polymerase elongation complex Newing T Tolun G DNA-DEPENDENT RNA POLYMERASE, TRANSCRIPTION, TRANSCRIPTION-DNA-RNA COMPLEX Newing TP Oakley AJ Miller M Dawson CJ Brown SHJ Bouwer JC Tolun G Lewis PJ Molecular basis for RNA polymerase-dependent transcription complex recycling by the helicase-like motor protein HelD. Nat Commun UK 11 6420 6420 2020 33339820 doi:10.1038/s41467-020-20157-5 2041-1723 6wvj FULLOVERLAP DNA-directed RNA polymerase elongation complex DNA-directed RNA polymerase elongation complex 0 1 2 3 4 5 6 7 0.344200 DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', DNA-directed RNA polymerase subunit omega/DNA Complex 1 1 2 3 4 Bacillus subtilis DNA, RNA 1 5 6 7 Escherichia coli BL21(DE3) DNA-directed RNA polymerase subunit alpha Bacillus subtilis (strain 168) 168 0.034842387 2 Escherichia coli BL21(DE3) LEVO MIEIEKPKIETVEISDDAKFGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTTIIL HIKKLALKIYSDEEKTLEIDVQGEGTVTAADITHDSDVEILNPDLHIATLGENASFRVRLTAQRGRGYTPADANKRDDQP IGVIPIDSIYTPVSRVSYQVENTRVGQVANYDKLTLDVWTDGSTGPKEAIALGSKILTEHLNIFVGLTDEAQHAEIMVEK EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGLRKDD P20429 2.7.7.6 DNA-directed RNA polymerase subunit beta Bacillus subtilis 0.133847938 1 Escherichia coli BL21(DE3) LEVO MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFLDEGLREMFQDISPIEDFTGNLSLEFIDYSLGEPKYPVEE SKERDVTYSAPLRVKVRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNGKKGFTA TVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLRNTLDKDNTENSDKALLEIYERL RPGEPPTVENAKSLLDSRFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAEKGQILDRRTLDKVLP YLENGIGFRKLYPNGGVVEDEVTLQSIKIFAPTDQEGEQVINVIGNAYIEEEIKNITPADIISSISYFFNLLHGVGDTDD IDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTNPLAEL THKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKVNRFGFIETPYRRVDPETGKVTGR IDYLTADEEDNYVVAQANARLDDEGAFIDDSIVARFRGENTVVSRNRVDYMDVSPKQVVSAATACIPFLENDDSNRALMG ANMQRQAVPLMQPEAPFVGTGMEYVSGKDSGAAVICKHPGIVERVEAKNVWVRRYEEVDGQKVKGNLDKYSLLKFVRSNQ GTCYNQRPIVSVGDEVVKGEILADGPSMELGELALGRNVMVGFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESEAR DTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVP HGGGGIIHDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPL GVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAKTVLYDGRTGEPFDNRVSVGIMYMIKL AHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGDNVP EPGVPESFKVLIKELQSLGMDVKILSGDEEEIEMRDLEDEEDAKQADGLALSGDEEPEETASADVERDVVTKE A0A2J0WBQ0 2.7.7.6 DNA-directed RNA polymerase subunit beta' Bacillus subtilis 0.134444953 1 Escherichia coli BL21(DE3) LEVO MLDVNNFEYMNIGLASPDKIRSWSFGEVKKPETINYRTLKPEKDGLFCERIFGPTKDWECHCGKYKRVRYKGVVCDRCGV EVTRAKVRRERMGHIELAAPVSHIWYFKGIPSRMGLVLDMSPRALEEVIYFASYVVTDPANTPLEKKQLLSEKEYRAYLD KYGNKFQASMGAEAIHKLLQDIDLVKEVDMLKEELKTSQGQRRTRAIKRLEVLEAFRNSGNKPSWMILDVLPVIPPELRP MVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPSIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHML KGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKMYQCGLPKEMALELFKPFVMKELVEKGLAHNIKSAKRKIERVQPEVWDV LESVIKEHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQAEARILMLAAQNIL NPKDGKPVVTPSQDMVLGNYYLTLERAGAVGEGMVFKNTDEALLAYQNGYVHLHTRVAVAANSLKNVTFTEEQRSKLLIT TVGKLVFNEILPESFPYMNEPTKSNIEEKTPDRFFLEKGADVKAVIAQQPINAPFKKGILGKIIAEIFKRFHITETSKML DRMKNLGFKYSTKAGITVGVSDIVVLDDKQEILEEAQSKVDNVMKQFRRGLITEEERYERVISIWSAAKDVIQGKLMKSL DELNPIYMMSDSGARGNASNFTQLAGMRGLMANPAGRIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYL TRRLVDVAQDVIIRETDCGTDRGILAKPLKEGTETIERLEERLIGRFARKQVKHPETGEVLVNENELIDEDKALEIVEAG IEEVWIRSAFTCNTPHGVCKRCYGRNLATGSDVEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGDDITQGLPRIQELF EARNPKGQATITEIDGTVVEINEVRDKQQEIVVQGAVETRSYTAPYNSRLKVAEGDKITRGQVLTEGSIDPKELLKVTDL TTVQEYLLHEVQKVYRMQGVEIGDKHVEVMVRQMLRKVRVIDAGDTDVLPGTLLDIHQFTEANKKVLLEGNRPATGRPVL LGITKASLETDSFLSAASFQETTRVLTDAAIKGKRDELLGLKENVIIGKLVPAGTGMMKYRKVKPVSNVQPTDDMVPVE A0A063XB23 2.7.7.6 DNA-directed RNA polymerase subunit omega Bacillus subtilis 0.0077669209999999995 1 Escherichia coli BL21(DE3) LEVO MLDPSIDSLMNKLDSKYTLVTVSARRAREMQIKKDQMIEHTISHKYVGKALEEIDAGLLSFEKEDRE A0A063XI46 2.7.7.6 DNA (5'-D(*TP*GP*TP*CP*GP*GP*GP*CP*GP*TP*CP*CP*GP*CP*GP*CP*GP*CP*C)-3') Escherichia coli BL21(DE3) BL21(DE3) 0.005814720999999999 1 (DT)(DG)(DT)(DC)(DG)(DG)(DG)(DC)(DG)(DT)(DC)(DC)(DG)(DC)(DG)(DC)(DG)(DC)(DC) DNA RNA (5'-R(P*GP*GP*CP*GP*CP*GP*CP*G)-3') Escherichia coli BL21(DE3) BL21(DE3) 0.0025966170000000003 1 GGCGCGCG DNA (5'-D(P*AP*CP*GP*CP*CP*CP*GP*AP*CP*A)-3') Escherichia coli BL21(DE3) BL21(DE3) 0.0029989839999999997 1 (DA)(DC)(DG)(DC)(DC)(DC)(DG)(DA)(DC)(DA) DNA ZINC ION 6.5409e-05 2 ZN MAGNESIUM ION 2.4305e-05 1 MG singleParticle particle 2.50 7.8 20.0 NH2C(CH2OH)3 Tris 150.0 NaCl Sodium Chloride 10.0 MgCl2 Magnesium Chloride 1.0 (HO2CCH2)2NCH2CH2N(CH2CO2H)2 EDTA 5.0 HSCH2CH(OH)CH(OH)CH2SH DTT Quantifoil R1.2/1.3 GOLD 300 GOLD HOLEY 50.0 GLOW DISCHARGE 32 AIR ETHANE 100 298 FEI VITROBOT MARK IV

Sample loading volume ranged between 2 and 3 microlitres. Samples were blotted for 5 seconds prior to vitrification..

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.6 2.8000000000000003 59500.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Quantum LS GATAN K2 SUMMIT (4k x 4k) COUNTING 3838 3710 1-40 2 5185 9.0 52.2 1 463519 The initial model was generated using the "3D initial model" algorithm in RELION 3.1 C1 3.36 FSC 0.143 CUT-OFF RELION 3.1 58854 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 emd_21920.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 166 172 188 61 65 55 188 172 166 157.92 144.48 139.44 90.0 90.0 90.0 Z Y X -5.7642713 10.3556385 -0.02620416 0.7741332 0.84 0.84 0.84000003 1.55 AUTHOR ::::EMDATABANK.org::::EMD-21920:::: Bacillus subtilis RNAP Elongation Complex REAL