2025-01-22 REL PDBe PDBe PDBe 2023-10-12 2024-10-23 2024-10-23 2025-01-22 Wellcome Trust 200835/Z/16/Z United Kingdom Wellcome Trust 222510/Z/21/Z United Kingdom Wellcome Trust WT106994/Z/15/Z United Kingdom Wellcome Trust 093305/Z/10/Z United Kingdom Wellcome Trust 060208/Z/00/Z United Kingdom Wellcome Trust 203141/Z/16/Z United Kingdom Carrique L Kus K Vasiljeva L Grimes JM RNA polymerase II, Rai1, Rat1, Spt5, DSIF, Termination, exoribonuclease, RNA BINDING PROTEIN Kus K Carrique L Kecman T Fournier M Hassanein SS Aydin E Kilchert C Grimes JM Vasiljeva L Nat Commun UK 16 10 10 2025 39746995 doi:10.1038/s41467-024-55063-7 2041-1723 8qsz FULLOVERLAP s. pombe RNA polymerase II in complex with DSIF and Rat1/Rai1 s. pombe RNA polymerase II in complex with DSIF and Rat1/Rai1 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 Schizosaccharomyces pombe DNA-directed RNA polymerase II subunit rpb1 Schizosaccharomyces pombe 0.194372625 1 LEVO MSGIQFSPSSVPLRRVEEVQFGILSPEEIRSMSVAKIEFPETMDESGQRPRVGGLLDPRLGTIDRQFKCQTCGETMADCP GHFGHIELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSNPKFNDTQRYRDPKNRLNAVWNVCKTKMVCDTGLSAGSDN FDLSNPSANMGHGGCGAAQPTIRKDGLRLWGSWKRGKDESDLPEKRLLSPLEVHTIFTHISSEDLAHLGLNEQYARPDWM IITVLPVPPPSVRPSISVDGTSRGEDDLTHKLSDIIKANANVRRCEQEGAPAHIVSEYEQLLQFHVATYMDNEIAGQPQA LQKSGRPLKSIRARLKGKEGRLRGNLMGKRVDFSARTVITGDPNLSLDELGVPRSIAKTLTYPETVTPYNIYQLQELVRN GPDEHPGAKYIIRDTGERIDLRYHKRAGDIPLRYGWRVERHIRDGDVVIFNRQPSLHKMSMMGHRIRVMPYSTFRLNLSV TSPYNADFDGDEMNMHVPQSEETRAEIQEITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTRNAVMNIMLWVP DWDGILPPPVILKPKVLWTGKQILSLIIPKGINLIRDDDKQSLSNPTDSGMLIENGEIIYGVVDKKTVGASQGGLVHTIW KEKGPEICKGFFNGIQRVVNYWLLHNGFSIGIGDTIADADTMKEVTRTVKEARRQVAECIQDAQHNRLKPEPGMTLRESF EAKVSRILNQARDNAGRSAEHSLKDSNNVKQMVAAGSKGSFINISQMSACVGQQIVEGKRIPFGFKYRTLPHFPKDDDSP ESRGFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMEDVMVRYDGTVRNAMGDIIQFAYGEDGLD ATLVEYQVFDSLRLSTKQFEKKYRIDLMEDRSLSLYMENSIENDSSVQDLLDEEYTQLVADRELLCKFIFPKGDARWPLP VNVQRIIQNALQIFHLEAKKPTDLLPSDIINGLNELIAKLTIFRGSDRITRDVQNNATLLFQILLRSKFAVKRVIMEYRL NKVAFEWIMGEVEARFQQAVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEILNVAKNIKTPSLT IYLMPWIAANMDLAKNVQTQIEHTTLSTVTSATEIHYDPDPQDTVIEEDKDFVEAFFAIPDEEVEENLYKQSPWLLRLEL DRAKMLDKKLSMSDVAGKIAESFERDLFTIWSEDNADKLIIRCRIIRDDDRKAEDDDNMIEEDVFLKTIEGHMLESISLR GVPNITRVYMMEHKIVRQIEDGTFERADEWVLETDGINLTEAMTVEGVDATRTYSNSFVEILQILGIEATRSALLKELRN VIEFDGSYVNYRHLALLCDVMTSRGHLMAITRHGINRAETGALMRCSFEETVEILMDAAASGEKDDCKGISENIMLGQLA PMGTGAFDIYLDQDMLMNYSLGTAVPTLAGSGMGTSQLPEGAGTPYERSPMVDSGFVGSPDAAAFSPLVQGGSEGREGFG DYGLLGAASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYS PTSPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS P36594 DNA-directed RNA polymerase II subunit RPB2 Schizosaccharomyces pombe 0.138027188 1 LEVO MSYEDYQYNETLTQEDCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDVTRRYEINFG QIYLSRPTMTEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNVPIGEEEWLVEEEDEEPSKVFIGKIPIMLR STFCILNGVSDSELYDLNECPYDQGGYFIINGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQ IKLMARNTENSGQTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAFVIQDKDIALDYI GKRGSTTGVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLA SLFRMLFRKMTRDVYKYMQKCVETNREFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSH LRRTNTPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEEWGLETLEDYNPSAS PNATKVFVNGVWLGVHRDPAHLTETLRSLRRRLDISAEVSIVRDIREKELRLFTDAGRICRPLFIVDNNPNSERRGELCI RKEHIQQLIEDKDRYDIDPEQRFGWTALVSSGLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYEVKEELDPAQRVKPAP NPHVHAWTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYYPQKPLATTRSMEY LKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSIFYRTYTDQEKKIGMTVMEEFERPVRSTTLRMKHGTYD KLEDDGLIAPGTRVSGEDIIIGKTAPIPLDHEELGQRTQLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRST RIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEGDATPFTDVT VEAVSKLLRSHGFQSRGFEVMYHGHTGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFG EMERDCQISHGCSSVLRERLFDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLPYAAKLLFQELMSMNI APRLFTKNHK Q02061 DNA-directed RNA polymerase II subunit RPB3 Schizosaccharomyces pombe 0.033748815999999994 1 LEVO MDSETHITIRNISKNSVDFVLTNTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAHRLGMIPLDSSNIDEPP PVGLEYTRNCDCDQYCPKCSVELFLNAKCTGEGTMEIYARDLVVSSNSSLGHPILADPKSRGPLICKLRKEQEISLRCIA KKGIAKEHAKWSPTSAVAFEYDPWNKLQHTDYWFENDADAEWPKSKNADWEEPPREGEPFNFQEEPRRFYMDVESVGSIP PNEIMVQGLRILQEKLAVLVRDLDEEQPTQLSANELNMEENAEMNWSPYQNGEENTW P37382 DNA-directed RNA polymerases I, II, and III subunit RPABC1 Schizosaccharomyces pombe 0.023954504 1 LEVO MSAEEKNIVRVFRAWKTAHQLVHDRGYGVSQAELDLTLDQFKAMHCGMGRNLDRTTLSFYAKPSNDSNKGTIYIEFAKEP SVGIKEMRTFVHTLGDHNHKTGILIYANSMTPSAAKIIATVTGQFTIETFQESDLIVNITHHELVPKHILLSPDEKKELL DRYKLRETQLPRIQLADPVARYLGLKRGEVVKIVRRSETSGRYNSYRICA Q09191 DNA-directed RNA polymerases I, II, and III subunit RPABC2 Schizosaccharomyces pombe 0.015742496999999998 1 LEVO MSDYEEDEAFGMDGAVMEEEVDELEMIDENGQSQQGVSHPGEPSTTVITEDVASSKTAQSGKAVAKEDRTTTPYMTKYER ARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKKIPLLVRRYLPDGSYEDWSVAELI P36595 DNA-directed RNA polymerase II subunit rpb7 Schizosaccharomyces pombe 0.019121982 1 LEVO MPFFLKELSLTISLHPSYFGPRMQDYLKAKLLADVEGTCSGQYGYIICVLDSNTIDIDKGRVVPGQGFAEFEVKYRAVLW RPFRGEVVDAIVTTVNKMGFFANIGPLNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKIVGTRTDATEIFA IATMKEDYLGVL O14459 DNA-directed RNA polymerases I, II, and III subunit RPABC3 Schizosaccharomyces pombe 0.014317317999999999 1 LEVO MSESVLLDEIFTVTSVDKQKYQRVSRITAVSGQNDMNLTLDINSQIYPLEKDATFSLQITSNLNSPDLKEAADYIMYGKV YRVEEAKDEKVSVYVSFGGLLMAIEGSHRKLYRLSLDHVYLLLRR Q92399 DNA-directed RNA polymerase II subunit RPB9,RBP9 Schizosaccharomyces pombe 0.0162538 1 LEVO MSNFQYCIECNNMLYPREDKVDRVLRLACRNCDYSEIAATSKVYRHELQSSNVENTTVSHDASTDPTLPRSDKECPRCHQ HEAVFYQTHSRRGDTMMTLIYVCVHCGFAFEEQGGGGGGDYKDHDGDYKDHDIDYKDDDDK O74635 DNA-directed RNA polymerases I, II, and III subunit RPABC5 Schizosaccharomyces pombe 0.008286801 1 LEVO MIIPIRCFSCGKVIGDKWDTYLTLLQEDNTEGEALDKLGLQRYCCRRMILTHVDLIEKLLCYNPLSKQKNL O13877 DNA-directed RNA polymerase II subunit RPB11 Schizosaccharomyces pombe 0.014143276 1 LEVO MNQPERYELIELMGLPKVTYELDSKSPNAAVVTLEKEDHTLANMLANQLLSDERVLFAGYKVPHPLNHNFILRVQTVEDC SPKQVIVDAAKSLITHLEEIKVNFMREWELKMISVEGVEMEFS P87123 DNA-directed RNA polymerases I, II, and III subunit RPABC4 Schizosaccharomyces pombe 0.007216495 1 LEVO MNHPTSTGGTAFNPPRPATMIYLCADCGARNTIQAKEVIRCRECGHRVMYKMRTKRMVQFEAR P48011 Transcription elongation factor spt5 Schizosaccharomyces pombe 0.123489242 1 Escherichia coli LEVO MKHHHHHHPMSDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKY GIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLAGSGSGSENLYFQGAMDTNSPKSIDKDANSTEVDAAEQDAASV KINSTRASPNGSDLLNDDSEAAKITTNEKQSSPVDSHNESPNDTTINKGEDGNENEVDNVNNNDKKEDEDNVEENEEEAD ANEEEEEDEEDDEEDEEDEDESGGGRRKRARHDRRNQFLDIEAEVDEDEEELEDEEDEIGREDGFIEEEVGADYVGDDRR HRELDRQRQELQSVDAERLAEEYREKYGRSQTVVGDTSNVPQRLLLPSVNDPNIWAVRCKIGKEKDIVFTIMRKAMDLQY TSSPLEIISAFQRDSLVGYIYVEARKQSHVLDALNGVLNVYTNNMILVPIKEMPDLLKVQKQVVELLPGAYVRIRRGKYA GDLAQVDNLSENGLTARVRIVPRIDYSDGLKRKNSATRPQARLFNESEAFKSNPSKFSKRGPRLFLFNNEEFEDGFLVKD IRISSLITEGVNPTLDEVSKFNPNNEDLDLSSLALSVKGGHAEFQPGDHVEVYVGEQTGVSGVVENVRGSVITMVSSDGL RLDVPSRGLRKRFRHGDYVKVIAGKYKDDTGMVVRISKDEVTFLSDTLMTELTVFSRDLGEASSAQAVNSAYELHDLVQL DVNTVACIFSVDRDTYKVIDQNGGVRTVLASQITMRHSNRRGVATDRNGAEIRIGDKVKEVGGEGKQGTILHIYRAFVFL HNRDIAENNGVFSARSRNVATIAAKGARISADLTKMNPALSNGPALPPVANLKRTIGRDKAIGATVRIRRGPMKGLLGVI KDTTDANARVELHTGNKMVTIPKENLLYTTKTGELISYTEFIERSRGIRPGSISTADGPNVPNWAQGARTPAVANGSRTP AWNTGSRTPAWNSGSKTPAWNSGSRTPAWNSGNKTPAWNAGSRTPAWNSGNKTPAWNVGNKTPAWNSGAKTPAWNAGNKT PSWNNGTKTPAWNANQTPMVANGTNTSWGQTPAYGGFSETNWDTEDNSKPYTAPTPGAWAAPTPGGWDDEEGDSPKYVPP SP O13936 DNA none template (34-MER) Schizosaccharomyces pombe 0.014917541 1 (DC)(DC)(DG)(DT)(DG)(DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(DA)(DG)(DG)(DG)(DA)(DA)(DA) (DT)(DG)(DG)(DT)(DT)(DT)(DG)(DT)(DG)(DT)(DC)(DT)(DG)(DC)(DT)(DT)(DA)(DT)(DC)(DG) (DG)(DT)(DA)(DG)(DA)(DG)(DT)(DG) DNA RNA (5'-R(P*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3') Schizosaccharomyces pombe 0.008245842 1 UGAAUCUAUUUCUUUUAUCGAGAGGU DNA template (40-MER) Schizosaccharomyces pombe 0.014659406 1 (DC)(DA)(DC)(DT)(DC)(DT)(DA)(DC)(DC)(DG)(DA)(DT)(DA)(DA)(DG)(DC)(DA)(DG)(DA)(DC) (DG)(DT)(DA)(DC)(DC)(DT)(DC)(DT)(DC)(DG)(DA)(DC)(DC)(DC)(DT)(DG)(DT)(DG)(DC)(DT) (DA)(DG)(DA)(DC)(DA)(DC)(DG)(DG) DNA 5'-3' exoribonuclease 2 Schizosaccharomyces pombe 0.102208312 1 Escherichia coli LEVO MGVPALFRLLSRKFAKVITPVIEAPTEKLPDGTEIEPDLSLPNPNGVECDNLYLDMNGIVHPCSHPEDRPAPETEDEMMV AVFEYTDRILAMVRPRQLLFIAIDGVAPRAKMNQQRSRRFRSSREAALKEEELQAFIEEAKQQGIPIDENATKKKSWDSN CITPGTPFMDTLAKSLRYYIINKLNSDPCWRNVRFILSDASVPGEGEHKIMEFIRSQRVKPEYDPNTHHVVYGLDAALIM LGLATHEPHFRVLREDVFFQQGSTKKTKEERLGIKRLDDVSETNKVPVKKPFIWLNVSILREYLEVELYVPNLPFPFDLE RAIDDWVFFIFFVGNDFLPHLPSLDIRDGAVERLTEIWRASLPHMGGYLTLDGSVNLARAEVILSAVGNQEDDIFKRLKQ QEDRRNENYRRRQQRESNQESESYVDNVVIQRSVETQSTEVVTSSKSTSVDTKPPKKTQKIDAPAPVDLVNLSEKTSNRS LGATNRELINNRAANRLGLSREAAAVSSVNKLAASALKAQLVSNETLQNVPLEDSIASSSAYEDTDSIESSTPVVHPIDT KVSNVGQKRKAPDSTEENENTDTVRLYEPGYRERYYEQKFHISPDEPEKIREAVKHYVHGLCWVLLYYYQGCPSWTWYYP YHYAPFAADFKDLASIDVKFELNQPFKPYEQLLGVLPAASKNNLPEKLQTLMTDENSEIIDFYPENFTIDLNGKKFEWQG VALLPFIDENRLLNAVSKIYPQLTEEESKRNEDGSTLLFISEHHPMFSELVKQLYSKKRQGKPLKLSGKMAHGLFGKVNT NDSVIPNVSVQCPIDVTSADALQKYGSIDDNQSISLVFEVPKSHFVHKSMLLRGVKMPNRVLTPEDINQVRAERSFSSRR NNGNSGSGHHHHHHHH P40848 ZINC ION 6.5409e-05 1 ZN singleParticle particle 0.7 7.5 25.0 HEPES 100.0 NaCl 0.05 Tween 20 CARBON HOLEY ETHANE 100 293 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 5.0 24.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 42.0 1 2200000 1 C1 2.67 FSC 0.143 CUT-OFF cryoSPARC V3.8 215000 MAXIMUM LIKELIHOOD cryoSPARC 3.8 MAXIMUM LIKELIHOOD cryoSPARC 3.8 10 95000.0 RELION 3.1 AlphaFold in silico model RIGID BODY FIT REAL emd_18643_msk_1.map emd_18643_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 352 352 352 0 0 0 352 352 352 369.59998 369.59998 369.59998 90.0 90.0 90.0 X Y Z -0.63916063 1.1338207 0.00084979576 0.051038135 1.05 1.05 1.05 AUTHOR ::::EMDATABANK.org::::EMD-18643:::: emd_18643_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 352 352 352 0 0 0 352 352 352 369.59998 369.59998 369.59998 90.0 90.0 90.0 X Y Z -0.64596343 1.17064 0.00084604725 0.05102157 1.05 1.05 1.05 AUTHOR ::::EMDATABANK.org::::EMD-18643::::