2025-07-09 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY em_admin em_software pdbx_entry_details _em_admin.last_update _em_software.name _pdbx_entry_details.has_protein_modification EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name PDBe PDBe 2023-08-25 2024-01-10 2024-01-10 2025-07-09 Max Planck Society Germany yeast cytoplasmic exosome-Ski2 complex degrading a RNA substrate Keidel A Koegel A Reichelt P Kowalinski E Schaefer IB Conti E Helicase, RNA binding, RNA degradation, HYDROLASE Keidel A Kogel A Reichelt P Kowalinski E Schafer IB Conti E Concerted structural rearrangements enable RNA channeling into the cytoplasmic Ski238-Ski7-exosome assembly. Mol.Cell US 83 4093 4105.e7 2023 37879335 doi:10.1016/j.molcel.2023.09.037 1097-2765 2168 MOCEFL 8qcf FULLOVERLAP yeast cytoplasmic exosome-Ski2 complex degrading a RNA substrate yeast cytoplasmic exosome-Ski2 complex degrading a RNA substrate 0 1 2 3 4 5 6 7 8 9 10 11 12 13 Saccharomyces cerevisiae Exosome complex component RRP45 Saccharomyces cerevisiae 0.034001858999999995 1 Escherichia coli LEVO MAKDIEISASESKFILEALRQNYRLDGRSFDQFRDVEITFGKEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEGLFVIS TEISPMAGSQFENGNITGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLM HFKKPDITVHGEQIIVHPVNEREPVPLGILHIPICVTFSFFNPQDTEENIKGETNSEISIIDATLKEELLRDGVLTVTLN KNREVVQVSKAGGLPMDALTLMKCCHEAYSIIEKITDQILQLLKEDSEKRNKYAAMLTSENAREI Q05636 Exosome complex component SKI6 Saccharomyces cerevisiae 0.027892041 1 Escherichia coli LEVO GPHMSRLEIYSPEGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVN ITKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDY ISGISVGLYDTTPLLDTNSLEENAMSTVTLGVVGKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRKHAQ KRVSNASAR P46948 Exosome complex component RRP43 Saccharomyces cerevisiae 0.044108999999999995 1 Escherichia coli LEVO MAESTTLETIEIHPITFPPEVLARISPELSLQRHLSLGIRPCLRKYEEFRDVAIENNTLSRYADAGNIDTKNNILGSNVL KSGKTIVITSITGGIIEETSASIKDLDDFGEEELFEVTKEEDIIANYASVYPVVEVERGRVGACTDEEMTISQKLHDSIL HSRILPKKALKVKAGVRSANEDGTFSVLYPDELEDDTLNETNLKMKRKWSYVLYAKIVVLSRTGPVFDLCWNSLMYALQS VKLPRAFIDERASDLRMTIRTRGRSATIRETYEIICDQTKSVPLMINAKNIAFASNYGIVELDPECQLQNSDNSEEEEVD IDMDKLNTVLIADLDTEAEETSIHSTISILAAPSGNYKQLTLMGGGAKITPEMIKRSLLLSRVRADDLSTRFNI P25359 RRP46 isoform 1 Saccharomyces cerevisiae 0.024659427999999997 1 Escherichia coli LEVO AASMSVQAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQELPTQLALEIIVRPAKGVATTREKVLEDKLRAVLTPL ITRHCYPRQLCQITCQILESGEDEAEFSLRELSCCINAAFLALVDAGIALNSMCASIPIAIIKDTSDIIVDPTAEQLKIS LSVHTLALEFVNGGKVVKNVLLLDSNGDFNEDQLFSLLELGEQKCQELVTNIRRIIQDNISPRLVV A0A6A5PYM9 Exosome complex component RRP42 Saccharomyces cerevisiae 0.029391516 1 Escherichia coli LEVO GPHMSLSVAEKSYLYDSLASTPSIRPDGRLPHQFRPIEIFTDFLPSSNGSSRIIASDGSECIVSIKSKVVDHHVENELLQ VDVDIAGQRDDALVVETITSLLNKVLKSGSGVDSSKLQLTKKYSFKIFVDVLVISSHSHPISLISFAIYSALNSTYLPKL ISAFDDLEVEELPTFHDYDMVKLDINPPLVFILAVVGNNMLLDPAANESEVANNGLIISWSNGKITSPIRSVALNDSNVK SFKPHLLKQGLAMVEKYAPDVVRSLENL Q12277 Exosome complex component MTR3 Saccharomyces cerevisiae 0.027573896 1 Escherichia coli LEVO MNVQDRRRLLGPAAAKPMAFSNTTTHVPEKKSTDLTPKGNESEQELSLHTGFIENCNGSALVEARSLGHQTSLITAVYGP RSIRGSFTSQGTISIQLKNGLLEKYNTNELKEVSSFLMGIFNSVVNLSRYPKSGIDIFVYLTYDKDLTNNPQDDDSQSKM TSSQISSLIPHCITSITLALADAGIELVDMAGAGEANGTVVSFIKNGEEIVGFWKDDGDDEDLLECLDRCKEQYNRYRDL MISCLMNQET P48240 Exosome complex component RRP40 Saccharomyces cerevisiae 0.026939687999999996 1 Escherichia coli LEVO GPDSMSTFIFPGDSFPVDPTTPVKLGPGIYCDPNTQEIRPVNTGVLHVSAKGKSGVQTAYIDYSSKRYIPSVNDFVIGVI IGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIECFDSTTGRDAGFGILEDGMII DVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNGKIWVKCEELSNTLACYRTIMECCQKNDTAAFKDIAKRQFKEILT VKEE Q08285 Exosome complex component RRP4 Saccharomyces cerevisiae 0.039929656 1 Escherichia coli LEVO TGGRSMSEVITITKRNGAFQNSSNLSYNNTGISDDENDEEDIYMHDVNSASKSESDSQIVTPGELVTDDPIWMRGHGTYF LDNMTYSSVAGTVSRVNRLLSVIPLKGRYAPETGDHVVGRIAEVGNKRWKVDIGGKQHAVLMLGSVNLPGGILRRKSESD ELQMRSFLKEGDLLNAEVQSLFQDGSASLHTRSLKYGKLRNGMFCQVPSSLIVRAKNHTHNLPGNITVVLGVNGYIWLRK TSQMDLARDTPSANNSSSIKSTGPTGAVSLNPSITRLEEESSWQIYSDENDPSISNNIRQAICRYANVIKALAFCEIGIT QQRIVSAYEASMVYSNVGELIEKNVMESIGSDILTAEKMRGNGN P38792 Exosome complex component CSL4 Saccharomyces cerevisiae 0.031911594 1 Escherichia coli LEVO GPHMACNFQFPEIAYPGKLICPQYGTENKDGEDIIFNYVPGPGTKLIQYEHNGRTLEAITATLVGTVRCEEEKKTDQEEE REGTDQSTEEEKSVDASPNDVTRRTVKNILVSVLPGTEKGRKTNKYANNDFANNLPKEGDIVLTRVTRLSLQRANVEILA VEDKPSPIDSGIGSNGSGIVAAGGGSGAATFSVSQASSDLGETFRGIIRSQDVRSTDRDRVKVIECFKPGDIVRAQVLSL GDGTNYYLTTARNDLGVVFARAANGAGGLMYATDWQMMTSPVTGATEKRKCAKPF P53859 Exosome complex exonuclease DIS3 Saccharomyces cerevisiae 0.11421405499999998 1 Escherichia coli LEVO GPDSMSVPAIAPRRKRLADGLSVTQKVFVRSRNGGATKIVREHYLRSDIPCLSRSCTKCPQIVVPDAQNELPKFILSDSP LELSAPIGKHYVVLDTNVVLQAIDLLENPNCFFDVIVPQIVLDEVRNKSYPVYTRLRTLCRDSDDHKRFIVFHNEFSEHT FVERLPNETINDRNDRAIRKTCQWYSEHLKPYDINVVLVTNDRLNREAATKEVESNIITKSLVQYIELLPNADDIRDSIP QMDSFDKDLERDTFSDFTFPEYYSTARVMGGLKNGVLYQGNIQISEYNFLEGSVSLPRFSKPVLIVGQKNLNRAFNGDQV IVELLPQSEWKAPSSIVLDSEHFDVNDNPDIEAGDDDDNNESSSNTTVISDKQRRLLAKDAMIAQRSKKIQPTAKVVYIQ RRSWRQYVGQLAPSSVDPQSSSTQNVFVILMDKCLPKVRIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVRDLGTIES AQAETEALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPEAVSKDPLLTKRKDLRDKLICSIDPPGCVDIDDALHA KKLPNGNWEVGVHIADVTHFVKPGTALDAEGAARGTSVYLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSANI VNVNFMKSVIRSREAFSYEQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRLEAGALNLASPEVKVHMDSETSDPNEVE IKKLLATNSLVEEFMLLANISVARKIYDAFPQTAMLRRHAAPPSTNFEILNEMLNTRKNMSISLESSKALADSLDRCVDP EDPYFNTLVRIMSTRCMMAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNK MDMICRNINRKHRNAQFAGRASIEYYVGQVMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEV EYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPITSKRKAELLLK Q08162 Superkiller protein 7 Saccharomyces cerevisiae 0.039242008 1 Escherichia coli LEVO GPDSMSAGLEVLFQGPDSATHIKFSKRDEDGKELAGATMELRDSSGKTISTWISDGQVKDFYLYPGKYTFVETAAPDGYE VATAITFTVNEQGQVTVNGSGSGSGSMSLLEQLARKRIEKSKGLLSADQSHSTSKSASLLERLHKNRETKDNNAETKRKD LKTLLAKDKVKRSDFTPNQHSVSLSLKLSALKKSNSDLEKQGKSVTLDSKENELPTKRKSPDDKLNLEESWKAIKEMNHY CFLKNDPCINQTDDFAFTNFIIKDKKNSLSTSIPLSSQNSSFLSLKKHNNELLGIFVPCNLPKTTRKVAIENFNRPSPDD IIQSAQLNAFNEKLENLNIKSVGSAWSHPQFEK Q08491 Antiviral helicase SKI2 Saccharomyces cerevisiae 0.11741267999999999 1 Trichoplusia ni LEVO MSEGFSSSSIQELYQSLKEITNNADVELFEDRITKLDFESTDEPKHANDIIKDRFLRPSNALPWSLLDMVQDVPHTSSPE DCSGKLDYKELLKVPDPINRTSYQFKRTGLEGKISGYKEEVDLKEVANANASNSLSITRSINHNQNSVRGSTAQLPFTPG GIPMKSVKTDSEQNGSSTMANATKLLHKDGQGLFDIPEGMNRGIKPMDSPAENEDQNGQFKELKQLNEIDNELDIRIEAN EAKLKEEEKSAKSISEEIMEEATEETTADNADDAEIDELLPIGIDFGRTKPVSKSVPVKKEWAHVVDLNHKIENFDELIP NPARSWPFELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRNMTKTIYTSPIKALSNQKFRDFKETFDDVN IGLITGDVQINPDANCLIMTTEILRSMLYRGADLIRDVEFVIFDQVHYVNDQDRGVVWEEVIIMLPQHVKFILLSATVPN TYEFANWIGRTKQKNIYVISTPKRPVPLEINIWAKKELIPVINQNSEFLEANFRKHKEILNGESAKGAPSKTDNGRGGST ARGGRGGSNTRDGRGGRGNSTRGGANRGGSRGAGAIGSNKRKFFTQDGPSKKTWPEIVNYLRKRELLPMVVFVFSKKRCE EYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLERGIAVHHGGLLPIVKELIEILFSKGFIKVLF ATETFAMGLNLPTRTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLDSTGTVIVMAYNSPLSIATFKEVTMGVPTRL QSQFRLTYNMILNLLRIEALRVEEMIKYSFSENAGSRGLSLLPDYEKRLAVLKDTEFIDQNHNVLLKGRVACEINSGYEL VLTELILDNFLGSFEPEEIVALLSVFVYEGKTREEEPPIVTPRLAKGKQRIEEIYKKMLCVFNTHQIPLTQDEAEFLDRK RFAMMNVVYEWARGLSFKEIMEMSPEAEGTVVRVITWLDEICREVKTASIIIGNSTLHMKMSRAQELIKRDIVFAASLYL P35207 3.6.4.13 RNA (5'hairpin 60U) Saccharomyces cerevisiae 0.024196508000000002 1 CUACCCCGAGAGGGGUAGUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU ADENOSINE-5'-TRIPHOSPHATE 0.000507181 1 ATP singleParticle particle 7.4 Quantifoil R2/1 ETHANE-PROPANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.6 2.2 GATAN K3 (6k x 4k) 63.36 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 2.55 FSC 0.143 CUT-OFF 338757 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_18329.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 306.432 306.432 306.432 90.0 90.0 90.0 X Y Z -3.000508 5.154519 0.0076187598 0.1563045 0.85120004 0.85120004 0.85120004 0.7 AUTHOR emd_18329_msk_1.map emd_18329_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 306.432 306.432 306.432 90.0 90.0 90.0 X Y Z -0.40786088 1.5090505 0.0076187598 0.06860007 0.85120004 0.85120004 0.85120004 AUTHOR map used to trace the flexible RNA backbone emd_18329_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 306.432 306.432 306.432 90.0 90.0 90.0 X Y Z -0.0017118774 1.7074817 0.0024371727 0.035396315 0.85120004 0.85120004 0.85120004 AUTHOR map sharpened with deepEMhancer software (tightTarget) emd_18329_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 306.432 306.432 306.432 90.0 90.0 90.0 X Y Z -0.54985386 1.6154861 0.006522936 0.08430791 0.85120004 0.85120004 0.85120004 AUTHOR emd_18329_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 306.432 306.432 306.432 90.0 90.0 90.0 X Y Z -0.4816133 1.6556267 0.006530103 0.084031865 0.85120004 0.85120004 0.85120004 AUTHOR