Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.3 angstrom (Part II: U1 snRNP region)

2024-03-27 REL PDBj PDBj PDBj 2018-05-16 2018-08-29 2018-08-29 2024-03-27 National Natural Science Foundation of China 31430020 China National Natural Science Foundation of China 31621092 China Ministry of Science and Technology (China) 2016YFA0501100 China Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.3 angstrom (Part II: U1 snRNP region) Bai R Wan R spliceosme, assemply, pre-B complex, U1 snRNP, Splicing Bai R Wan R Yan C Lei J Shi Y Structures of the fully assembledSaccharomyces cerevisiaespliceosome before activation Science US 360 1423 1429 2018 29794219 doi:10.1126/science.aau0325 1095-9203 0038 SCIEAS EMD-6972 other EM volume

tri-snRNP and U2 snRNP parts of pre-B complex

5zwn FULLOVERLAP Pre-B spliceosomal complex Pre-B spliceosomal complex 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Saccharomyces cerevisiae pre-mRNA Saccharomyces cerevisiae S288c 0.007130372 1 AAAAAAAAAAGGUAUGUAUUAA U1 snRNA Saccharomyces cerevisiae S288c 0.182114516 1 AUACUUACCUUAAGAUAUCAGAGGAGAUCAAGAAGUCCUACUGAUCAAACAUGCGCUUCCAAUAGUAGAAGGACGUUAAG CAUUUAUCAUUGAACUAUAAUUGUUCAUUGAAGUCAUUGAUGCAAACUCCUUGGUCACACACACAUACGGCGCGGAAGGC GUGUUUGCUGACGUUUCCAUUCCCUUGUUUCAAUCAUUGGUUAAUCCCUUGAUUCCUUUGGGGAUUUUUGGGUUAAACUG AUUUUUGGGGCCCUUUGUUUCUUCUGCCUGGAGAAGUUUGACACCAAAUUCAAAUUGGUGUUAGGGGAGCUGGGGCCUUU CAAAAGAGAGCUUUGUAGAGGCAUUCUUUUUGACUACUUUUCUCUAGCGUGCCAUUUUAGUUUUUGACGGCAGAUUCGAA UGAACUUAAGUUUAUGAUGAAGGUAUGGCUGUUGAGAUUAUUUGGUCGGGAUUGUAGUUUGAAGAUGUGCUCUUUUGAGC AGUCUCAACUUUGCUCGUUCCCGUUAUGGGAAAAAUUUUGGAAGGUCUUGGUAGGAACGGGUGGAUCUUAUAAUUUUUGA UUUAUUUU U1 small nuclear ribonucleoprotein 70 kDa homolog Saccharomyces cerevisiae S288c S288c 0.034506148 1 LEVO MNYNLSKYPDDVSRLFKPRPPLSYKRPTDYPYAKRQTNPNITGVANLLSTSLKHYMEEFPEGSPNNHLQRYEDIKLSKIK NAQLLDRRLQNWNPNVDPHIKDTDPYRTIFIGRLPYDLDEIELQKYFVKFGEIEKIRIVKDKITQKSKGYAFIVFKDPIS SKMAFKEIGVHRGIQIKDRICIVDIERGRTVKYFKPRRLGGGLGGRGYSNRDSRLPGRFASASTSNPAERNYAPRLPRRE TSSSAYSADRYGSSTLDARYRGNRPLLSAATPTAAVTSVYKSRNSRTRESQPAPKEAPDY Q00916 U1 small nuclear ribonucleoprotein C Saccharomyces cerevisiae S288c S288c 0.027106015999999997 1 LEVO MTRYYCEYCHSYLTHDTLSVRKSHLVGKNHLRITADYYRNKARDIINKHNHKRRHIGKRGRKERENSSQNETLKVTCLSN KEKRHIMHVKKMNQKELAQTSIDTLKLLYDGSPGYSKVFVDANRFDIGDLVKASKLPQRANEKSAHHSFKQTSRSRDETC ESNPFPRLNNPKKLEPPKILSQWSNTIPKTSIFYSVDILQTTIKESKKRMHSDGIRKPSSANGYKRRRYGN Q05900 U1 small nuclear ribonucleoprotein A Saccharomyces cerevisiae S288c S288c 0.034438105000000004 1 LEVO MSALYFQNLPSRPANKENYTRLLLKHINPNNKYAINPSLPLPHNKLQISSQPLMLLDDQMGLLEVSISRSSKMTNQAFLT FVTQEEADRFLEKYTTTALKVQGRKVRMGKARTNSLLGLSIEMQKKKGNDETYNLDIKKVLKARKLKRKLRSDDICAKKF RLKRQIRRLKHKLRSRKVEEAEIDRIVKEFETRRLENMKSQQENLKQSQKPLKRAKVSNTMENPPNKVLLIQNLPSGTTE QLLSQILGNEALVEIRLVSVRNLAFVEYETVADATKIKNQLGSTYKLQNNDVTIGFAK P32605 U1 small nuclear ribonucleoprotein component PRP42 Saccharomyces cerevisiae S288c S288c 0.06522201999999999 1 LEVO MDKYTALIHDENFSTLTLNVSRYPKSLAYWEKLLNYIVKASAPICKSTEPQLLKLIRCTYSSMLNEFPYLENYYIDFALL EYKLGNVSMSHKIFQRGLQAFNQRSLLLWTSYLKFCNNVISHQKQLFKKYETAEEYVGLHFFSGEFWDLYLEQISSRCTS SKKYWNVLRKILEIPLHSFSKFYALWLQRIDDIMDLKQLSQLTSKDELLKKLKIDINYSGRKGPYLQDAKKKLKKITKEM YMVVQYQVLEIYSIFESKIYINYYTSPETLVSSDEIETWIKYLDYTITLQTDSLTHLNFQRALLPLAHYDLVWIKYSKWL INSKNDLLGAKNVLLMGLKFSLKKTEIIKLLYSVICKLNEYVLLRNLLEKIESSYSDNVENVDDFEIFWDYLQFKTFCQN SLYSSRYSDSQSNGLLNKELFDKVWKRLSCKEKKSGQEILLNNLVQFYSKDTVEFVEKNIFQKIIEFGWEYYLQNGMFWN CYCRLIYFDTSRSYLDKRQYIVRKIWPQIDKKFAQSVLPSLTEFCESYFPEEMDTLEEMFTEEP Q03776 Pre-mRNA-processing factor 39 Saccharomyces cerevisiae S288c S288c 0.074834742 1 LEVO MPDETNFTIEDIEPRPDALRGLDTQFLQDNTALVQAYRGLDWSDISSLTQMVDVIEQTVVKYGNPNDSIKLALETILWQI LRKYPLLFGFWKRFATIEYQLFGLKKSIAVLATSVKWFPTSLELWCDYLNVLCVNNPNETDFIRNNFEIAKDLIGKQFLS HPFWDKFIEFEVGQKNWHNVQRIYEYIIEVPLHQYARFFTSYKKFLNEKNLKTTRNIDIVLRKTQTTVNEIWQFESKIKQ PFFNLGQVLNDDLENWSRYLKFVTDPSKSLDKEFVMSVFDRCLIPCLYHENTWMMYIKWLTKKNISDEVVVDIYQKANTF LPLDFKTLRYDFLRFLKRKYRSNNTLFNNIFNETVSRYLKIWPNDILLMTEYLCMLKRHSFKNSLDQSPKEILEKQTSFT KILETSITNYINNQIDAKVHLQTLINDKNLSIVVVELIKTTWLVLKNNMQTRKYFNLYQKNILIKNSVPFWLTYYKFEKS NVNFTKLNKFIRELGVEIYLPTTVMNDILTDYKTFYLTHSNIVTYESSIIDSNTFDPILYPELKMSNPKYDPVLNTTANV DWHKKTEWKEAGHIGITTERPQISNSIIECNSGTLIQKPISLPNFRNLEKINQVKINDLYTEEFLKEGK P39682 Protein NAM8 Saccharomyces cerevisiae S288c S288c 0.05701083999999999 1 LEVO MSYKQTTYYPSRGNLVRNDSSPYTNTISSETNNSSTSVLSLQGASNVSLGTTGNQLYMGDLDPTWDKNTVRQIWASLGEA NINVRMMWNNTLNNGSRSSMGPKNNQGYCFVDFPSSTHAANALLKNGMLIPNFPNKKLKLNWATSSYSNSNNSLNNVKSG NNCSIFVGDLAPNVTESQLFELFINRYASTSHAKIVHDQVTGMSKGYGFVKFTNSDEQQLALSEMQGVFLNGRAIKVGPT SGQQQHVSGNNDYNRSSSSLNNENVDSRFLSKGQSFLSNGNNNMGFKRNHMSQFIYPVQQQPSLNHFTDPNNTTVFIGGL SSLVTEDELRAYFQPFGTIVYVKIPVGKCCGFVQYVDRLSAEAAIAGMQGFPIANSRVRLSWGRSAKQTALLQQAMLSNS LQVQQQQPGLQQPNYGYIPSSTCEAPVLPDNNVSSTMLPGCQILNYSNPYANANGLGSNNFSFYSNNNATNTQATSLLAD TSSMDLSGTGGQQVIMQGSEAVVNSTNAMLNRLEQGSNGFMFA Q00539 56 kDa U1 small nuclear ribonucleoprotein component Saccharomyces cerevisiae S288c S288c 0.056575277 1 LEVO MRPRRRGLAYHHTKPKGQLSQGHYPTTSNDGQRRKVGNSEAFQSFDIWKNLDRIRSTKKNAGQFIKGSLLILPMRTEDKQ QFDECMDELHKYISKDILRCYPQKEQKDEGMLFYIVLKDFNILDSCFVLSVLLAFQKRLWMAPSEKSYFRVPKNINLTGS FYLPKNIETGRGHIITSYRREQPSSSIVEVGFNVVPDFQQFQVKACHVSKFMNELSNFFSQVEFGKCEANVINYFKREYN RTYSQISLALYELPLIGDGLFDIKSYISKTRPIIETSKAQMIKHISEMKAYNEISGLQGDQFPRQQRPLSNSPSSNSISS SQTIEAGATSYQTQPQRHAVNKPSNVLNSSNRHSGPKTFEDGRYSEGNKPGFMTQDEIKQHCIGTIKASMDAVKKKSSYQ ILKTYVRCPRQNYIDIVYQNLNDLRSKTNCNIVVLNLNNLHESQMWLESLNTTNYTIFAQAPHPSTIRVISIGGVGEYIV KALELILNILEH Q03782 Small nuclear ribonucleoprotein-associated protein B Saccharomyces cerevisiae S288c S288c 0.02242699 1 LEVO MSKIQVAHSSRLANLIDYKLRVLTQDGRVYIGQLMAFDKHMNLVLNECIEERVPKTQLDKLRPRKDSKDGTTLNIKVEKR VLGLTILRGEQILSTVVEDKPLLSKKERLVRDKKEKKQAQKQTKLRKEKEKKPGKIAKPNTANAKHTSSNSREIAQPSSS RYNGGNDNIGANRSRFNNEAPPQTRKFQPPPGFKRK P40018 Small nuclear ribonucleoprotein Sm D1 Saccharomyces cerevisiae S288c S288c 0.016296798 1 LEVO MKLVNFLKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTDVKLTLPQPRLNKLNSNGIAMASLYLTGGQQPTASDNIA SLQYINIRGNTIRQIILPDSLNLDSLLVDQKQLNSLRRSGQIANDPSKKRRRDFGAPANKRPRRGL Q02260 Small nuclear ribonucleoprotein Sm D2 Saccharomyces cerevisiae S288c S288c 0.012876066 1 LEVO MSSQIIDRPKHELSRAELEELEEFEFKHGPMSLINDAMVTRTPVIISLRNNHKIIARVKAFDRHCNMVLENVKELWTEKK GKNVINRERFISKLFLRGDSVIVVLKTPVE Q06217 Small nuclear ribonucleoprotein Sm D3 Saccharomyces cerevisiae S288c S288c 0.011240138999999998 1 LEVO MTMNGIPVKLLNEAQGHIVSLELTTGATYRGKLVESEDSMNVQLRDVIATEPQGAVTHMDQIFVRGSQIKFIVVPDLLKN APLFKKNSSRPMPPIRGPKRR P43321 Small nuclear ribonucleoprotein E Saccharomyces cerevisiae S288c S288c 0.010385097999999999 1 LEVO MSNKVKTKAMVPPINCIFNFLQQQTPVTIWLFEQIGIRIKGKIVGFDEFMNVVIDEAVEIPVNSADGKEDVEKGTPLGKI LLKGDNITLITSAD Q12330 Small nuclear ribonucleoprotein F Saccharomyces cerevisiae S288c S288c 0.009669945 1 LEVO MSESSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLY IRELPN P54999 Small nuclear ribonucleoprotein G Saccharomyces cerevisiae S288c S288c 0.008490808999999998 1 LEVO MVSTPELKKYMDKKILLNINGSRKVAGILRGYDIFLNVVLDDAMEINGEDPANNHQLGLQTVIRGNSIISLEALDAI P40204 U1 small nuclear ribonucleoprotein component SNU71 Saccharomyces cerevisiae S288c S288c 0.07138345299999999 1 LEVO MRDIVFVSPQLYLSSQEGWKSDSAKSGFIPILKNDLQRFQDSLKHIVDARNSLSETLLNSNDDGSIHNSDQNTGLNKDKE ASIADNNSANKCATSSSRYQELKQFLPISLDQQIHTVSLQGVSSSFSRGQIESLLDHCLNLALTETQSNSALKVEAWSSF SSFLDTQDIFIRFSKVDEDEAFVNTLNYCKALFAFIRKLHEDFKIELHLDLNTKEYVEDRTGTIPSVKPEKASEFYSVFK NIEDQTDERNSKKEQLDDSSTQYKVDTNTLSDLPSDALDQLCKDIIEFRTKVVSIEKEKKMKSTYEESRRQRHQMQKVFD QIRKNHSGAKGSANTEEEDTNMEDEDEEDDTEDDLALEKRKEERDLEESNRRYEDMLHQLHSNTEPKIKSIRADIMSAEN YEEHLEKNRSLYLKELLHLANDVHYDHHRSFKEQEERRDEEDRAKNGNAKELAPIQLSDGKAISAGKAAAITLPEGTVKS ENYNADKNVSESSEHVKIKFDFKKAIDHSVESSSEDEGYRESELPPTKPSERSAAEDRLPFTADELNIRLTNLKESRYVD ELVREFLGVYEDELVEYILENIRVNQSKQALLNELRETFDEDGETIADRLWSRKEFRLG P53207 Protein LUC7 Saccharomyces cerevisiae S288c S288c 0.030245884999999997 1 LEVO MSTMSTPAAEQRKLVEQLMGRDFSFRHNRYSHQKRDLGLHDPKICKSYLVGECPYDLFQGTKQSLGKCPQMHLTKHKIQY EREVKQGKTFPEFEREYLAILSRFVNECNGQISVALQNLKHTAEERMKIQQVTEELDVLDVRIGLMGQEIDSLIRADEVS MGMLQSVKLQELISKRKEVAKRVRNITENVGQSAQQKLQVCEVCGAYLSRLDTDRRLADHFLGKIHLGYVKMREDYDRLM KNNRTTNASKTATTLPGRRFV Q07508 U1 snRNP Saccharomyces cerevisiae S288c 0.003500827 1 LEVO AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 Saccharomyces cerevisiae S288c S288c 0.06673318799999998 1 LEVO MARPIDVSQLIAGINKKKGLDENTSGKISKPRFLNKQERSKQERLKENEESLTPTQSDSAKVEIKKVNSRDDSFFNETND KKRNPSKQNGSKFHFSWNESEDTLSGYDPIVSTRAIDLLWKGKTPKNAAESSYMGKHWTEKSLHEMNERDWRILKEDYAI VTKGGTVENPLRNWEELNIIPRDLLRVIIQELRFPSPTPIQRITIPNVCNMKQYRDFLGVASTGSGKTLAFVIPILIKMS RSPPRPPSLKIIDGPKALILAPTRELVQQIQKETQKVTKIWSKESNYDCKVISIVGGHSLEEISFSLSEGCDILVATPGR LIDSLENHLLVMKQVETLVLDEADKMIDLGFEDQVTNILTKVDINADSAVNRQTLMFTATMTPVIEKIAAGYMQKPVYAT IGVETGSEPLIQQVVEYADNDEDKFKKLKPIVAKYDPPIIIFINYKQTADWLAEKFQKETNMKVTILHGSKSQEQREHSL QLFRTNKVQIMIATNVAARGLDIPNVSLVVNFQISKKMDDYIHRIGRTGRAANEGTAVSFVSAAEDESLIRELYKYVRKH DPLNSNIFSEAVKNKYNVGKQLSNEIIY P23394 3.6.4.13 ZINC ION 6.5409e-05 3 ZN singleParticle cell 7.9 Quantifoil R1.2/1.3 COPPER ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) 50.0 1 C1 FOURIER SPACE 3.4 FSC 0.143 CUT-OFF RELION 2.0 500657 PROJECTION MATCHING PROJECTION MATCHING emd_6973.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 535.2 535.2 535.2 90.0 90.0 90.0 X Y Z -0.19564165 0.34690544 0.00067012367 0.009224686 1.338 1.338 1.338 0.045 AUTHOR ::::EMDATABANK.org::::EMD-6973:::: U1 snRNP region of the spliceosomal pre-B complex