Yeast U1 snRNP with humanized U1C Zinc-Finger domain

2025-06-04 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name STRUCTURE_SUMMARY em_admin em_software pdbx_entry_details _em_admin.last_update _em_software.name RCSB RCSB 2024-02-20 2024-05-15 2024-05-15 2025-06-04 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM145289 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01GM126157 (R.Z.) United States Yeast U1 snRNP with humanized U1C Zinc-Finger domain Shi SS Kuang ZL Zhao R U1snRNP, U1C humanization, SPLICING Chalivendra S Shi S Li X Kuang Z Giovinazzo J Zhang L Rossi J Wang J Saviola AJ Welty R Liu S Vaeth KF Zhou ZH Hansen KC Taliaferro JM Zhao R Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast. Rna UK 30 1070 1088 2024 38688558 doi:10.1261/rna.079917.123 1469-9001 2122 RNARFU 8w2o FULLOVERLAP U1snRNP U1snRNP 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 Saccharomyces cerevisiae S288C U1 small nuclear ribonucleoprotein 70 kDa homolog Saccharomyces cerevisiae S288C 0.034506148 1 Saccharomyces cerevisiae S288C LEVO MNYNLSKYPDDVSRLFKPRPPLSYKRPTDYPYAKRQTNPNITGVANLLSTSLKHYMEEFPEGSPNNHLQRYEDIKLSKIK NAQLLDRRLQNWNPNVDPHIKDTDPYRTIFIGRLPYDLDEIELQKYFVKFGEIEKIRIVKDKITQKSKGYAFIVFKDPIS SKMAFKEIGVHRGIQIKDRICIVDIERGRTVKYFKPRRLGGGLGGRGYSNRDSRLPGRFASASTSNPAERNYAPRLPRRE TSSSAYSADRYGSSTLDARYRGNRPLLSAATPTAAVTSVYKSRNSRTRESQPAPKEAPDY Q00916 U1 small nuclear ribonucleoprotein C Saccharomyces cerevisiae S288C 0.027084949 1 Saccharomyces cerevisiae S288C LEVO MPKFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYRNKARDIINKHNHKRRHIGKRGRKERENSSQNETLKVTCLSN KEKRHIMHVKKMNQKELAQTSIDTLKLLYDGSPGYSKVFVDANRFDIGDLVKASKLPQRANEKSAHHSFKQTSRSRDETC ESNPFPRLNNPKKLEPPKILSQWSNTIPKTSIFYSVDILQTTIKESKKRMHSDGIRKPSSANGYKRRRYGN Q05900 U1 small nuclear ribonucleoprotein A Saccharomyces cerevisiae S288C 0.040413961 1 Saccharomyces cerevisiae S288C LEVO MSALYFQNLPSRPANKENYTRLLLKHINPNNKYAINPSLPLPHNKLQISSQPLMLLDDQMGLLEVSISRSSKMTNQAFLT FVTQEEADRFLEKYTTTALKVQGRKVRMGKARTNSLLGLSIEMQKKKGNDETYNLDIKKVLKARKLKRKLRSDDICAKKF RLKRQIRRLKHKLRSRKVEEAEIDRIVKEFETRRLENMKSQQENLKQSQKPLKRAKVSNTMENPPNKVLLIQNLPSGTTE QLLSQILGNEALVEIRLVSVRNLAFVEYETVADATKIKNQLGSTYKLQNNDVTIGFAKGRRIPGLINPWKRRWKKNFIAV SAANRFKKISSSGALDYDIPTTASENLYFQ P32605 U1 small nuclear ribonucleoprotein component PRP42 Saccharomyces cerevisiae S288C 0.06522201999999999 1 Saccharomyces cerevisiae S288C LEVO MDKYTALIHDENFSTLTLNVSRYPKSLAYWEKLLNYIVKASAPICKSTEPQLLKLIRCTYSSMLNEFPYLENYYIDFALL EYKLGNVSMSHKIFQRGLQAFNQRSLLLWTSYLKFCNNVISHQKQLFKKYETAEEYVGLHFFSGEFWDLYLEQISSRCTS SKKYWNVLRKILEIPLHSFSKFYALWLQRIDDIMDLKQLSQLTSKDELLKKLKIDINYSGRKGPYLQDAKKKLKKITKEM YMVVQYQVLEIYSIFESKIYINYYTSPETLVSSDEIETWIKYLDYTITLQTDSLTHLNFQRALLPLAHYDLVWIKYSKWL INSKNDLLGAKNVLLMGLKFSLKKTEIIKLLYSVICKLNEYVLLRNLLEKIESSYSDNVENVDDFEIFWDYLQFKTFCQN SLYSSRYSDSQSNGLLNKELFDKVWKRLSCKEKKSGQEILLNNLVQFYSKDTVEFVEKNIFQKIIEFGWEYYLQNGMFWN CYCRLIYFDTSRSYLDKRQYIVRKIWPQIDKKFAQSVLPSLTEFCESYFPEEMDTLEEMFTEEP Q03776 Pre-mRNA-processing factor 39 Saccharomyces cerevisiae S288C 0.074834742 1 Saccharomyces cerevisiae S288C LEVO MPDETNFTIEDIEPRPDALRGLDTQFLQDNTALVQAYRGLDWSDISSLTQMVDVIEQTVVKYGNPNDSIKLALETILWQI LRKYPLLFGFWKRFATIEYQLFGLKKSIAVLATSVKWFPTSLELWCDYLNVLCVNNPNETDFIRNNFEIAKDLIGKQFLS HPFWDKFIEFEVGQKNWHNVQRIYEYIIEVPLHQYARFFTSYKKFLNEKNLKTTRNIDIVLRKTQTTVNEIWQFESKIKQ PFFNLGQVLNDDLENWSRYLKFVTDPSKSLDKEFVMSVFDRCLIPCLYHENTWMMYIKWLTKKNISDEVVVDIYQKANTF LPLDFKTLRYDFLRFLKRKYRSNNTLFNNIFNETVSRYLKIWPNDILLMTEYLCMLKRHSFKNSLDQSPKEILEKQTSFT KILETSITNYINNQIDAKVHLQTLINDKNLSIVVVELIKTTWLVLKNNMQTRKYFNLYQKNILIKNSVPFWLTYYKFEKS NVNFTKLNKFIRELGVEIYLPTTVMNDILTDYKTFYLTHSNIVTYESSIIDSNTFDPILYPELKMSNPKYDPVLNTTANV DWHKKTEWKEAGHIGITTERPQISNSIIECNSGTLIQKPISLPNFRNLEKINQVKINDLYTEEFLKEGK P39682 Protein NAM8 Saccharomyces cerevisiae S288C 0.05701083999999999 1 Saccharomyces cerevisiae S288C LEVO MSYKQTTYYPSRGNLVRNDSSPYTNTISSETNNSSTSVLSLQGASNVSLGTTGNQLYMGDLDPTWDKNTVRQIWASLGEA NINVRMMWNNTLNNGSRSSMGPKNNQGYCFVDFPSSTHAANALLKNGMLIPNFPNKKLKLNWATSSYSNSNNSLNNVKSG NNCSIFVGDLAPNVTESQLFELFINRYASTSHAKIVHDQVTGMSKGYGFVKFTNSDEQQLALSEMQGVFLNGRAIKVGPT SGQQQHVSGNNDYNRSSSSLNNENVDSRFLSKGQSFLSNGNNNMGFKRNHMSQFIYPVQQQPSLNHFTDPNNTTVFIGGL SSLVTEDELRAYFQPFGTIVYVKIPVGKCCGFVQYVDRLSAEAAIAGMQGFPIANSRVRLSWGRSAKQTALLQQAMLSNS LQVQQQQPGLQQPNYGYIPSSTCEAPVLPDNNVSSTMLPGCQILNYSNPYANANGLGSNNFSFYSNNNATNTQATSLLAD TSSMDLSGTGGQQVIMQGSEAVVNSTNAMLNRLEQGSNGFMFA Q00539 56 kDa U1 small nuclear ribonucleoprotein component Saccharomyces cerevisiae S288C 0.056575277 1 Saccharomyces cerevisiae S288C LEVO MRPRRRGLAYHHTKPKGQLSQGHYPTTSNDGQRRKVGNSEAFQSFDIWKNLDRIRSTKKNAGQFIKGSLLILPMRTEDKQ QFDECMDELHKYISKDILRCYPQKEQKDEGMLFYIVLKDFNILDSCFVLSVLLAFQKRLWMAPSEKSYFRVPKNINLTGS FYLPKNIETGRGHIITSYRREQPSSSIVEVGFNVVPDFQQFQVKACHVSKFMNELSNFFSQVEFGKCEANVINYFKREYN RTYSQISLALYELPLIGDGLFDIKSYISKTRPIIETSKAQMIKHISEMKAYNEISGLQGDQFPRQQRPLSNSPSSNSISS SQTIEAGATSYQTQPQRHAVNKPSNVLNSSNRHSGPKTFEDGRYSEGNKPGFMTQDEIKQHCIGTIKASMDAVKKKSSYQ ILKTYVRCPRQNYIDIVYQNLNDLRSKTNCNIVVLNLNNLHESQMWLESLNTTNYTIFAQAPHPSTIRVISIGGVGEYIV KALELILNILEH Q03782 U1 small nuclear ribonucleoprotein component SNU71 Saccharomyces cerevisiae S288C 0.00597476 1 Saccharomyces cerevisiae S288C LEVO MRDIVFVSPQLYLSSQEGWKSDSAKSGFIPILKNDLQRFQDSLKHIVDARNS P53207 Protein LUC7 Saccharomyces cerevisiae S288C 0.030245884999999997 1 Saccharomyces cerevisiae S288C LEVO MSTMSTPAAEQRKLVEQLMGRDFSFRHNRYSHQKRDLGLHDPKICKSYLVGECPYDLFQGTKQSLGKCPQMHLTKHKIQY EREVKQGKTFPEFEREYLAILSRFVNECNGQISVALQNLKHTAEERMKIQQVTEELDVLDVRIGLMGQEIDSLIRADEVS MGMLQSVKLQELISKRKEVAKRVRNITENVGQSAQQKLQVCEVCGAYLSRLDTDRRLADHFLGKIHLGYVKMREDYDRLM KNNRTTNASKTATTLPGRRFV Q07508 Small nuclear ribonucleoprotein-associated protein B Saccharomyces cerevisiae S288C 0.02242699 1 Saccharomyces cerevisiae S288C LEVO MSKIQVAHSSRLANLIDYKLRVLTQDGRVYIGQLMAFDKHMNLVLNECIEERVPKTQLDKLRPRKDSKDGTTLNIKVEKR VLGLTILRGEQILSTVVEDKPLLSKKERLVRDKKEKKQAQKQTKLRKEKEKKPGKIAKPNTANAKHTSSNSREIAQPSSS RYNGGNDNIGANRSRFNNEAPPQTRKFQPPPGFKRK P40018 Small nuclear ribonucleoprotein Sm D1 Saccharomyces cerevisiae S288C 0.016296798 1 Saccharomyces cerevisiae S288C LEVO MKLVNFLKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTDVKLTLPQPRLNKLNSNGIAMASLYLTGGQQPTASDNIA SLQYINIRGNTIRQIILPDSLNLDSLLVDQKQLNSLRRSGQIANDPSKKRRRDFGAPANKRPRRGL Q02260 Small nuclear ribonucleoprotein Sm D2 Saccharomyces cerevisiae S288C 0.012876066 1 Saccharomyces cerevisiae S288C LEVO MSSQIIDRPKHELSRAELEELEEFEFKHGPMSLINDAMVTRTPVIISLRNNHKIIARVKAFDRHCNMVLENVKELWTEKK GKNVINRERFISKLFLRGDSVIVVLKTPVE Q06217 Small nuclear ribonucleoprotein Sm D3 Saccharomyces cerevisiae S288C 0.011240138999999998 1 Saccharomyces cerevisiae S288C LEVO MTMNGIPVKLLNEAQGHIVSLELTTGATYRGKLVESEDSMNVQLRDVIATEPQGAVTHMDQIFVRGSQIKFIVVPDLLKN APLFKKNSSRPMPPIRGPKRR P43321 Small nuclear ribonucleoprotein E Saccharomyces cerevisiae S288C 0.010385097999999999 1 Saccharomyces cerevisiae S288C LEVO MSNKVKTKAMVPPINCIFNFLQQQTPVTIWLFEQIGIRIKGKIVGFDEFMNVVIDEAVEIPVNSADGKEDVEKGTPLGKI LLKGDNITLITSAD Q12330 Small nuclear ribonucleoprotein F Saccharomyces cerevisiae S288C 0.009669945 1 Saccharomyces cerevisiae S288C LEVO MSESSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLY IRELPN P54999 Small nuclear ribonucleoprotein G Saccharomyces cerevisiae S288C 0.008490808999999998 1 Saccharomyces cerevisiae S288C LEVO MVSTPELKKYMDKKILLNINGSRKVAGILRGYDIFLNVVLDDAMEINGEDPANNHQLGLQTVIRGNSIISLEALDAI P40204 ACT1 pre-mRNA Saccharomyces cerevisiae S288C 0.059778190999999994 1 GGAUCCGAUAUCCGUACACCAUCAGGGUACGAGCUAGCCCAUGGCGUACACCAUCAGGGUACGACUAGUAGAUCUCGUAC ACCAUCAGGGUACGGAAUUGUCUAGACUUUUAGAUUUUUCACGCUUACUGCUUUUUUCUUCCCAAGAUCGAAAAUUUACU GAAUUAACAAUGGAUUCUGGUAUGUUC U1 snRNA Saccharomyces cerevisiae S288C 0.182114516 1 AUACUUACCUUAAGAUAUCAGAGGAGAUCAAGAAGUCCUACUGAUCAAACAUGCGCUUCCAAUAGUAGAAGGACGUUAAG CAUUUAUCAUUGAACUAUAAUUGUUCAUUGAAGUCAUUGAUGCAAACUCCUUGGUCACACACACAUACGGCGCGGAAGGC GUGUUUGCUGACGUUUCCAUUCCCUUGUUUCAAUCAUUGGUUAAUCCCUUGAUUCCUUUGGGGAUUUUUGGGUUAAACUG AUUUUUGGGGCCCUUUGUUUCUUCUGCCUGGAGAAGUUUGACACCAAAUUCAAAUUGGUGUUAGGGGAGCUGGGGCCUUU CAAAAGAGAGCUUUGUAGAGGCAUUCUUUUUGACUACUUUUCUCUAGCGUGCCAUUUUAGUUUUUGACGGCAGAUUCGAA UGAACUUAAGUUUAUGAUGAAGGUAUGGCUGUUGAGAUUAUUUGGUCGGGAUUGUAGUUUGAAGAUGUGCUCUUUUGAGC AGUCUCAACUUUGCUCGUUCCCGUUAUGGGAAAAAUUUUGGAAGGUCUUGGUAGGAACGGGUGGAUCUUAUAAUUUUUGA UUUAUUUU singleParticle particle 1.5 7.9 120.0 NaCl sodium chloride 20.0 C8H18N2O4S Hepes 2.0 C14H24N2O10 EGTA

20 mM Hepes, pH7.9, 120 mM KCl, 2 mM EGTA

EMS Lacey Carbon COPPER 400 CARBON HOLEY 20.0 PLASMA CLEANING 20 OTHER ETHANE 100 277 FEI VITROBOT MARK IV

The grids were obtained with the chamber at 100% humidity, 2.5 s blotting time, -6 blotting force and 15 s wait time and flash-frozen into liquid ethane with a Vitrobot Mark IV (Thermo Fisher Scientific).

This sample is monodisperse

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.8 2.2 GATAN K3 (6k x 4k) 1.0 1 NONE 3.49 FSC 0.143 CUT-OFF 138997 OTHER OTHER emd_43753.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 640 640 640 0 0 0 640 640 640 531.2 531.2 531.2 90.0 90.0 90.0 Y X Z -1.2842387 2.1316335 0.00021066514 0.031006655 0.83000004 0.83000004 0.83000004 0.08 AUTHOR ::::EMDATABANK.org::::EMD-43753:::: emd_43753_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 640 640 640 0 0 0 640 640 640 531.2 531.2 531.2 90.0 90.0 90.0 X Y Z -0.49311742 1.1983935 0.00087636476 0.046439156 0.83000004 0.83000004 0.83000004 AUTHOR ::::EMDATABANK.org::::EMD-43753:::: emd_43753_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 640 640 640 0 0 0 640 640 640 531.2 531.2 531.2 90.0 90.0 90.0 X Y Z -0.47001043 1.1833445 0.000868655 0.046491805 0.83000004 0.83000004 0.83000004 AUTHOR ::::EMDATABANK.org::::EMD-43753::::