2024-07-17 REL PDBe PDBe PDBe 2021-06-03 2021-08-11 2021-08-11 2024-07-17 German Research Foundation (DFG) SFB 860 Germany The U2 part of Saccharomyces cerevisiae spliceosomal pre-A complex (delta BS-A ACT1) Zhang Z Rigo N S. cerevisiae, pre-A complex, Prp5, U1 snRNP, U2 snRNP, prespliceosome, SPLICING Zhang Z Rigo N Dybkov O Fourmann JB Will CL Kumar V Urlaub H Stark H Luhrmann R Structural insights into how Prp5 proofreads the pre-mRNA branch site. Nature UK 596 296 300 2021 34349264 doi:10.1038/s41586-021-03789-5 1476-4687 0006 NATUAS 7oqb FULLOVERLAP S. cerevisiae spliceosomal pre-A complex S. cerevisiae spliceosomal pre-A complex 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 Saccharomyces cerevisiae U2 snRNP component HSH155 Saccharomyces cerevisiae 0.11016667200000001 1 LEVO MSHPIQFVNANNSDKSHQLGGQYSIPQDLRENLQKEAARIGENEKDVLQEKMETRTVQNREDSYHKRRFDMKFEPDSDTQ TVTSSENTQDAVVPRKRKSRWDVKGYEPPDESSTAVKENSDSALVNVEGIHDLMFFKPSDHKYFADVISKKPIDELNKDE KKERTLSMLLLKIKNGNTASRRTSMRILTDKAVTFGPEMIFNRLLPILLDRSLEDQERHLMIKTIDRVLYQLGDLTKPYV HKILVVAAPLLIDEDPMVRSTGQEIITNLSTVAGLKTILTVMRPDIENEDEYVRNVTSRAAAVVAKALGVNQLLPFINAA CHSRKSWKARHTGIKIVQQIGILLGIGVLNHLTGLMSCIKDCLMDDHVPVRIVTAHTLSTLAENSYPYGIEVFNVVLEPL WKGIRSHRGKVLSSFLKAVGSMIPLMDPEYAGYYTTEAMRIIRREFDSPDDEMKKTILLVLQKCSAVESITPKFLREEIA PEFFQKFWVRRVALDRPLNKVVTYTTVTLAKKLGCSYTIDKLLTPLRDEAEPFRTMAVHAVTRTVNLLGTADLDERLETR LIDALLIAFQEQTNSDSIIFKGFGAVTVSLDIRMKPFLAPIVSTILNHLKHKTPLVRQHAADLCAILIPVIKNCHEFEML NKLNIILYESLGEVYPEVLGSIINAMYCITSVMDLDKLQPPINQILPTLTPILRNKHRKVEVNTIKFVGLIGKLAPTYAP PKEWMRICFELLELLKSTNKEIRRSANATFGFIAEAIGPHDVLVALLNNLKVQERQLRVCTAVAIGIVAKVCGPYNVLPV IMNEYTTPETNVQNGVLKAMSFMFEYIGNMSKDYIYFITPLLEDALTDRDLVHRQTASNVITHLALNCSGTGHEDAFIHL MNLLIPNIFETSPHAIMRILEGLEALSQALGPGLFMNYIWAGLFHPAKNVRKAFWRVYNNMYVMYQDAMVPFYPVTPDNN EEYIEELDLVL P49955 ACT1 pre-mRNA (delta-BS-A) Saccharomyces cerevisiae 0.10120896099999999 1 AUGGAUUCUGGUAUGUUCUAGCGCUUGCACCAUCCCAUUUAACUGUAAGAAGAAUUGCACGGUCCCAAUUGCUCGAGAGA UUUCUCUUUUACCUUUUUUUACUAUUUUUCACUCUCCCAUAACCUCCUAUAUUGACUGAUCUGUAAUAACCACGAUAUUA UUGGAAUAAAUAGGGGCUUGAAAUUUGGAAAAAAAAAAAAAACUGAAAUAUUUUCGUGAUAAGUGAUAGUGAUAUUCUUC UUUUAUUUGCUACUGUUACUAAGUCUCAUGUACUACAUCGAUUGCUUCAUUCUUUUUGUUGCUAUAUUAUAUGUUUAG Pre-mRNA-splicing factor PRP11 Saccharomyces cerevisiae 0.031324467 1 LEVO MNYLEGVGSKKGGGGIASESQFNLQRRKEVESLLSKGENVPYTFQDEKDDQVRSNPYIYKNHSGKLVCKLCNTMHMSWSS VERHLGGKKHGLNVLRRGISIEKSSLGREGQTTHDFRQQQK(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)IIEAKQSLKNNGTIPVCKIATVKNPKNGSVGLAIQ VNYSSEVKENSVDSDDKAKVPPLIRIVSGLELSDTKQKGKKFLVIAYEPFENIAIELPPNEILFSENNDMDNNNDGVDEL NKKCTFWDAISKLYYVQFFFKQAEQEQADV Q07350 Pre-mRNA-splicing factor PRP21 Saccharomyces cerevisiae 0.033111512 1 LEVO MEPEDTQLKEDIKTTVNYIKQHGVEFENKLLEDERFSFIKKDDPLHEYYTKLMNEPTDTVSGEDNDRKSEREIARPPDFL FSQYDTGISRRDMEVIKLTARYYAKDKSIVEQMISKDGEARLNFMNSSHPLHKTFTDFVAQYKRVYSFTGQEIKKSKRTI LDNCFERTQYWEFEKDKDREHDKLVELCKIQFAAIPWDKFTQVAKFSIPEDTEIFEGSLDLEQMRLRRVQTGIKLFDSIK PTNEEEKIVSDQGKQKGGDSKGKKRKIRAVGETRLKKSKK P32524 Pre-mRNA-splicing factor PRP9 Saccharomyces cerevisiae 0.063126445 1 LEVO MNLLETRRSLLEEMEIIENAIAERIQRNPELYYHYIQESSKVFPDTKLPRSSLIAENKIYKFKKVKRKRKQIILQQHEIN IFLRDYQEKQQTFNKINRPEETQEDDKDLPNFERKLQQLEKELKNEDENFELDINSKKDKYALFSSSSDPSRRTNILSDR ARDLDLNEIFTRDEQYGEYMELEQFHSLWLNVIKRGDCSLLQFLDILELFLDDEKYLLTPPMDRKNDRYMAFLLKLSKYV ETFFFKSYALLDAAAVENLIKSDFEHSYCRGSLRSEAKGIYCPFCSRWFKTSSVFESHLVGKIHKKNESKRRNFVYSEYK LHRYLKYLNDEFSRTRSFVERKLAFTANERMAEMDILTQKYEAPAYDSTEKEGAEQVDGEQRDGQLQEEHLSGKSFDMPL GPDGLPMPYWLYKLHGLDREYRCEICSNKVYNGRRTFERHFNEERHIYHLRCLGIEPSSVFKGITKIKEAQELWKNMQGQ SQLTSIAAVPPKPNPSQLKVPTELELEEEDEEGNVMSKKVYDELKKQGLV P19736 Pre-mRNA-splicing factor RDS3 Saccharomyces cerevisiae 0.012283572999999999 1 LEVO MSRHQFDLIMCLKQPGVQTGLLCEKCDGKCPICDSYVRPKRKVRVCENCSFGKQAKNCIICNLNVGVNDAFYCWECCRLG KDKDGCPRILNLGSNRLDRHFEKKKKV Q06835 Cold sensitive U2 snRNA suppressor 1 Saccharomyces cerevisiae 0.050339879 1 LEVO MARTKSRKRSGNNQNKNASVVNNKAEIAAMIDARRLEQKKKGGVTNSKGKTNKVVDAKLEKEFKDVLQRFQVQENDTPKE ITKDEKNNHVVIVEKNPVMNRKHTAEDELEDTPSDGIEEHLSARKRRKTEKPSLSQLKSQVPYPQIIEWYDCDARYPGLL ASIKCTKNVIPVPSHWQSKKEYLSGRSLLGKRPFELPDIIKKTNIEQMRSTLPQSGLDGQDEKSLKEASRARVQPKMGAL DLDYKKLHDVFFKIGANWKPDHLLCFGDVYYENRNLFEETNWKRMVDHKRPGRISQELRAIMNLPEGQLPPWCMKMKDIG LPTGYPDLKIAGLNWDITNLKGDVYGKIIPNHHSRSKKQGRNYFGALISFETPEFENSKEDTQANAENGRQDDKIDDEVE HKLDHFQEDISEVTSAEEKLERNEEESEKQLYTVLK Q02554 Pre-mRNA-splicing factor RSE1 Saccharomyces cerevisiae 0.153956781 1 LEVO MWGGGKMAVVSLSPHTAKMRKLFGQASTTMAYDGLKREAERRTRSDHNITMVAKDDELYLYHLTLKKQTNFVHSCIGHFV DLEAGSKREQSQLCVATETHLELYDTADGELKLIAKFQNLFATITSMKSLDLPHSGSRAKASNWPTFLALTSDSGNLSIV QIIMHAGALRLKTLVNQPLTRTTLRRVSPISYMEIDPNGRCIILSSVEQNKLCFLVDYAQKLRISSPLEIIRPHMVTLDM AVVDVNFNNPCFVTLEIDNAATQLSVHLIFYVLELGLNHIVKKADYLVNPSANFVLSLPDLSRYNITTSLSDNNYDADYD TLFNPFVVIGFENHILVKDMNGFFSLKVEIPKRSITNSRHKNVTIISGIVQKLKNDFFVLLQSNHGDLFKLTVSPDTNDR NRPLVQLSYFDTIQNSHQLHIFKNGYLFALSEMNNNFLFQFEKLGVEKNDFSNVLTSKDPNKSLVFEPSIKLQNLSILSQ QLNLNPSIKSQIVSDSPLSIATKHFTNNKIITLTNAVNYSNLISTSLPPNATKLWLIPDPATTGDNNTLLFITFPKKTMI LQIDNESMEELTPDEATRSAFKLSQDTTIHTCLMGSHSIIQVCTAELRHIVPTGKSRYSNKLTWVPPAGIRIVCATSSKT QLIISLSNYELVYFKIDVSSDSLIELTTHPELDTMPSKVAIVQDTQHADLLAIADNEGMIKIMSLKDQKEDFLTVISLQL VSEKISDMIMVRDSSIGQLNLHVGLENGVYMKFHIGDVDGSFTDIKRRFLGLKPVSLSYLREISVSLNNEEEEEEEEDDD DEKEEEEINSSGAKWMSCVVCHSSSTWVSYTWKNVWTIRQLKDQNMLSCSKFVNADVAINGVCSISSSGRLNIGRVSNFP TLDNWFHVHESSVNKQENGGGDESNEEEEDEMEEEMEMLQISTFRPRTILSFPNNPKSILFIDNHSGKKQCRISLQIDGE CLKFGSSDHLYKILDDIDCVSAAIIDFTRQADHLIICAGDKRLLTYKILVNKDKLSFDIELLHQTEIISPIHAMLKFKNF LLTAMGSTIVLYGLGKKQLLRRSVTQTPVSITKIVSMHQWNYERLAVGDIHESVTLFIWDPAGNVFIPYVDDSVKRHVTV LKFLDEATVIGADRYGNAWTLRSPPECEKIMSNHDPSELSNGAIKYPLDVITLQQKLPNTYDCKFKFQLLNHFFVNDIIT DFHILDSLSNSDRPGCIYMGLQGTVGCFIPLLSKGNVFMMGNIENIMAEADDTFYLDYESRKKNNNMRKEDDEEESGSVV LQGRHGIEDEIICEGSCSILGRDHQEYRSYYAPVRKVIDGDLCENFLRLSLNEQEFLAKNLKSVQVEDIIQTINEVRTNY M Q04693 Protein HSH49 Saccharomyces cerevisiae 0.024534151999999997 1 LEVO MNYSADSGNTVYVGNIDPRITKEQLYELFIQINPVLRIKYPKDKVLQAYQGYAFIEFYNQGDAQYAIKIMNNTVRLYDRL IKVRQVTNSTGTTNLPSNISKDMILPIAKLFIKNLADSIDSDQLVKIFNKFGKLIREPEIFYLSNGKLKCAYVYFEDFEK ADLAIKSLNNQLVANNRITVDYAFKENGKGNAKYGDDVDRLLNKEALKHNMLK Q99181 RDS3 complex subunit 10 Saccharomyces cerevisiae 0.009888207 1 LEVO MAEKQRQLKLQKIYKQKYIGLGDESTTREQWQRNVRNDTLNTLQGHSASLEYVSLSRGDLSIRDTRIHLLKSMSPGYKAY LREE P0C074 U2 small nuclear ribonucleoprotein A' Saccharomyces cerevisiae 0.027232252 1 LEVO MKFTPSIVIDAPQYYVDHFNGKYNVDKCVILRDLQLETDSESMPSSLKHLTKPTHILDLTNNDLIMIPDLSRRDDIHTLL LGRNNIVEVDGRLLPMNVQNLTLSNNSIRRFEDLQRLRRAPRTLKNLTLIGNQVCHLANYREHVLRLVPHLETLDFQNVT AEERKSAMSFPRQADGDTLGPVNTAIRDNGSRDKTMEIMNLVVSKMTVERRNELKKQLAEATSLEEIARLEKLLSGGV Q08963 U2 small nuclear ribonucleoprotein B'' Saccharomyces cerevisiae 0.012850944 1 LEVO MVEPARKKQRIDRDTHHTVAEPVTEAKNTLYVSQLNEKINMQRLRVNLFLLFATFGEVLKVSMNFKKQRGQAFITMRTID QASLAQISLNGERFFGKPLKVEFSKSETKTL P40567 Small nuclear ribonucleoprotein-associated protein B Saccharomyces cerevisiae 0.02242699 1 LEVO MSKIQVAHSSRLANLIDYKLRVLTQDGRVYIGQLMAFDKHMNLVLNECIEERVPKTQLDKLRPRKDSKDGTTLNIKVEKR VLGLTILRGEQILSTVVEDKPLLSKKERLVRDKKEKKQAQKQTKLRKEKEKKPGKIAKPNTANAKHTSSNSREIAQPSSS RYNGGNDNIGANRSRFNNEAPPQTRKFQPPPGFKRK P40018 Small nuclear ribonucleoprotein Sm D1 Saccharomyces cerevisiae 0.016296798 1 LEVO MKLVNFLKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTDVKLTLPQPRLNKLNSNGIAMASLYLTGGQQPTASDNIA SLQYINIRGNTIRQIILPDSLNLDSLLVDQKQLNSLRRSGQIANDPSKKRRRDFGAPANKRPRRGL Q02260 Small nuclear ribonucleoprotein Sm D2 Saccharomyces cerevisiae 0.012876066 1 LEVO MSSQIIDRPKHELSRAELEELEEFEFKHGPMSLINDAMVTRTPVIISLRNNHKIIARVKAFDRHCNMVLENVKELWTEKK GKNVINRERFISKLFLRGDSVIVVLKTPVE Q06217 Small nuclear ribonucleoprotein Sm D3 Saccharomyces cerevisiae 0.011240138999999998 1 LEVO MTMNGIPVKLLNEAQGHIVSLELTTGATYRGKLVESEDSMNVQLRDVIATEPQGAVTHMDQIFVRGSQIKFIVVPDLLKN APLFKKNSSRPMPPIRGPKRR P43321 Small nuclear ribonucleoprotein E Saccharomyces cerevisiae 0.01027001 1 LEVO MSNKVKTKAMVPPINCIFNFLQQQTPVTIWLFEQIGIRIKGKIVGFDEFMNVVIDEAVEIPVNSADGKEDVEKGTPLGKI LLKGDNITLITSA Q12330 Small nuclear ribonucleoprotein F Saccharomyces cerevisiae 0.009669945 1 LEVO MSESSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLY IRELPN P54999 Small nuclear ribonucleoprotein G Saccharomyces cerevisiae 0.008490808999999998 1 LEVO MVSTPELKKYMDKKILLNINGSRKVAGILRGYDIFLNVVLDDAMEINGEDPANNHQLGLQTVIRGNSIISLEALDAI P40204 Pre-mRNA-processing ATP-dependent RNA helicase PRP5 Saccharomyces cerevisiae 0.09651212499999999 1 LEVO METIDSKQNINRESLLEERRKKLAKWKQKKAQFDAQKEHQTSRNDIVTNSLEGKQTTEKFTERQERVKEELRKRKNEFRK SDEPVSVKPSKKKSKRSKVKKKISFDFSDDDDSEIGVSFRSKEHIQKAPEHDNEKDPLDEFMTSLKEEKMSNSKGMYDRG DILDVEDQLFELGGTDDEDVEDNTDNSNIAKIAKLKAKKRVKQIYYSPEELEPFQKNFYIESETVSSMSEMEVEELRLSL DNIKIKGTGCPKPVTKWSQLGLSTDTMVLITEKLHFGSLTPIQSQALPAIMSGRDVIGISKTGSGKTISYLLPLLRQVKA QRPLSKHETGPMGLILAPTRELALQIHEEVTKFTEADTSIRSVCCTGGSEMKKQITDLKRGTEIVVATPGRFIDILTLND GKLLSTKRITFVVMDEADRLFDLGFEPQITQIMKTVRPDKQCVLFSATFPNKLRSFAVRVLHSPISITINSKGMVNENVK QKFRICHSEDEKFDNLVQLIHERSEFFDEVQSENDGQSSDVEEVDAKAIIFVSSQNICDFISKKLLNAGIVTCAIHAGKP YQERLMNLEKFKREKNSILLCTEVLSRGLNVPEVSLVIIYNAVKTFAQYVHTTGRTARGSRSGTAITLLLHDELSGAYIL SKAMRDEEIKALDPLQAKELQEMSAKFESGMKKGKFRLSKGFGGKGLENIKSKREEAQNKDLELKKNDKRSDDLEKKISN PREGHDSVSESSALIPRLNYELFKESTDGSIIFYAKVYINDLPQIVRWEATKNTTLLFIKHETGCSITNKGKFYPEGKEP KNENDEPKLYLLIEGQDEKDIQLSIELLEQKVKEGVVKAASLSLKSTKY P21372 U2 snRNA Saccharomyces cerevisiae 0.376267406 1 ACGAAUCUCUUUGCCUUUUGGCUUAGAUCAAGUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGAAAUGACCUCAAUGAG GCUCAUUACCUUUUAAUUUGUUACAAUACACAUUUUUUGGCACCCAAAAUAAUAAAAUGGACGGGAAGAGACUUUUUAAG CAAGUUGUUUUCCGCUAAUGUCAGGUCUCACUACUUUUUGCUGCUAUUUUUCUUCGCUCAUGGUUUCUUCAUAAGGCGUU UUUAUGAUGGUUUUUCGAAAUUGGUUUUUGAGACGACGGUUGCUCAAGGUUAUUGUUUUUGUUUUCUUCUGGUUGUUUUC UAUUUUCUUUUUUUUAGCUUUCUGUUUCUCCCUUAGUUUGGCUUUUUGCUUCAUACUCUUCCCUGUCUUUCCGAGCCGUU UAUGUCCAACGCGGGAUUUGGUUUUUCUUUAUCGAUGGGAAGAAAUGGUGCUAUAGUAGGUUGGGAGAUAAUAUUUAUGG UAUGGGGUGCUAGUGCGGAUGGGGCGCUCUUAUUGUUGAUUUCUUCGCUCGUCUUCUUUUUCUGGUGGCGCUGCAAGAGG AAGUUUUUCGACUUUGUUAUGAUUUUUGGUUUGCAAGGAAAGGUGUCUUACGAUUCUUUUUUUGAUGUAAUAGGAUAAGC UUGCUUAUCCCCCAAGUAUCGGCCAAAGUUGUUGAUUUUCCUUUUGAAGUGUCCUCGGUUUGAGGGGGUGUAGGGUGGGG UUGGUCUACAAUAAGAGUGUUCCAUUGUUAACGUGCUGGCGUCUUUUACUAUAUUUUUUUUCCCAGUUUAUUUUGUGCUU AUUUUCUCAUUGAGGAGAAGGAGCUCUUCUCGCAGGAUAUAAAUGGAGGUUUGCUAAAGGGGAGGAGAUGUGUUUGUGAG AAUACUGCUGAGAGAGUUCUGGAAGAGAAAAAAAGGAGGCAAUGGAAGGCGUUUGCUGGGAAAAGAGAAGAGCCAUGACU GCAUCUGUUGUUUCAAGGCCAGUUUUAUUAACCGCCUAUGUCAUAGAGGCGUUUUUUUUGGAGGGAUUUGAAGAAUGCCG GCGGCAUCAAGAAACGGACUUGAUGGUUGACGCCUGUUUUUAAAGUUAGAGACGUCGCGACCCUCGCACUUGUGGAGUCG UUCUUGACUUUUACUUUGGUCGCUUGAUGUUUCUCUCGUCUUCCCGUUCGCUCUU Z36099.1 singleParticle particle 7.9 Quantifoil R3.5/1 COPPER CARBON CONTINUOUS ETHANE 100 277 FEI VITROBOT MARK I FEI TITAN KRIOS SPOT SCAN BRIGHT FIELD FIELD EMISSION GUN 300 100.0 0.01 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON III (4k x 4k) INTEGRATING 1.02 44.0 1
Ab initio model
 9.0 FSC 0.143 CUT-OFF RELION 3.0 160894 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0 emd_13028.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 220 220 220 0 0 0 220 220 220 510.4 510.4 510.4 90.0 90.0 90.0 X Y Z -0.043786433 0.10472864 0.00027660112 0.0045616603 2.32 2.32 2.32 0.038 AUTHOR emd_13028_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 220 220 220 0 0 0 220 220 220 510.4 510.4 510.4 90.0 90.0 90.0 X Y Z -0.03246495 0.074758366 0.00060178223 0.0042253393 2.32 2.32 2.32 AUTHOR emd_13028_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 220 220 220 0 0 0 220 220 220 510.4 510.4 510.4 90.0 90.0 90.0 X Y Z -0.033827998 0.07129752 -0.000048579957 0.0041241446 2.32 2.32 2.32 AUTHOR