2024-05-15 REL PDBe PDBe PDBe 2018-02-20 2018-03-14 2018-03-21 2024-05-15 ERC EXORICO Belgium Structure of the nuclear RNA exosome Schuller JM Falk S RNA exosome, Ribosome, pre-ribosome, Mtr4, Helicase, RNA Schuller JM Falk S Fromm L Hurt E Conti E Structure of the nuclear exosome captured on a maturing preribosome. Science US 360 219 222 2018 29519915 doi:10.1126/science.aar5428 1095-9203 0038 SCIEAS 6fsz FULLOVERLAP Nuclear RNA exosome Nuclear RNA exosome 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Nuclear RNA exosome 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Saccharomyces cerevisiae nucleic acid 1 1 Saccharomyces cerevisiae RNA (5'-R(P*AP*AP*AP*AP*UP*UP*UP*AP*AP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') Saccharomyces cerevisiae 0.007158136999999999 1 AAAAUUUAAAUUUUUUUUUUUUU Exosome complex component RRP45 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.03379959 1 Escherichia coli LEVO KDIEISASESKFILEALRQNYRLDGRSFDQFRDVEITFGKEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEGLFVISTE ISPMAGSQFENGNITGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHF KKPDITVHGEQIIVHPVNEREPVPLGILHIPICVTFSFFNPQDTEENIKGETNSEISIIDATLKEELLRDGVLTVTLNKN REVVQVSKAGGLPMDALTLMKCCHEAYSIIEKITDQILQLLKEDSEKRNKYAAMLTSENAREI Q05636 Exosome complex component SKI6 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.027794925999999998 1 Escherichia coli LEVO GHMSRLEIYSPEGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNI TKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYI SGISVGLYDTTPLLDTNSLEENAMSTVTLGVVGKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRKHAQK RVSNASAR P46948 Exosome complex component RRP43 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.043977805 1 Escherichia coli LEVO AESTTLETIEIHPITFPPEVLARISPELSLQRHLSLGIRPCLRKYEEFRDVAIENNTLSRYADAGNIDTKNNILGSNVLK SGKTIVITSITGGIIEETSASIKDLDDFGEEELFEVTKEEDIIANYASVYPVVEVERGRVGACTDEEMTISQKLHDSILH SRILPKKALKVKAGVRSANEDGTFSVLYPDELEDDTLNETNLKMKRKWSYVLYAKIVVLSRTGPVFDLCWNSLMYALQSV KLPRAFIDERASDLRMTIRTRGRSATIRETYEIICDQTKSVPLMINAKNIAFASNYGIVELDPECQLQNSDNSEEEEVDI DMDKLNTVLIADLDTEAEETSIHSTISILAAPSGNYKQLTLMGGGAKITPEMIKRSLLLSRVRADDLSTRFNI P25359 Exosome complex component RRP46 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.026913988 1 Escherichia coli LEVO GHGNNKEPNTKNRLDSAEKKKKMSVQAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQELPTQLALEIIVRPAKGV ATTREKVLEDKLRAVLTPLITRHCYPRQLCQITCQILESGEDEAEFSLRELSCCINAAFLALVDAGIALNSMCASIPIAI IKDTSDIIVDPTAEQLKISLSVHTLALEFVNGGKVVKNVLLLDSNGDFNEDQLFSLLELGEQKCQELVTNIRRIIQDNIS PRLVV P53256 Exosome complex component RRP42 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.029294398 1 Escherichia coli LEVO GHMSLSVAEKSYLYDSLASTPSIRPDGRLPHQFRPIEIFTDFLPSSNGSSRIIASDGSECIVSIKSKVVDHHVENELLQV DVDIAGQRDDALVVETITSLLNKVLKSGSGVDSSKLQLTKKYSFKIFVDVLVISSHSHPISLISFAIYSALNSTYLPKLI SAFDDLEVEELPTFHDYDMVKLDINPPLVFILAVVGNNMLLDPAANESEVANNGLIISWSNGKITSPIRSVALNDSNVKS FKPHLLKQGLAMVEKYAPDVVRSLENL Q12277 Exosome complex component MTR3 Saccharomyces cerevisiae ATCC 204508 / S288c 0.027559868999999997 1 Escherichia coli LEVO MNVQDRRRLLGPAAAKPMAFSNTTTHVPEKKSTDLTPKGNESEQELSLHTGFIENCNGSALVEARSLGHQTSLISAVYGP RSIRGSFTSQGTISIQLKNGLLEKYNTNELKEVSSFLMGIFNSVVNLSRYPKSGIDIFVYLTYDKDLTNNPQDDDSQSKM TSSQISSLIPHCITSITLALADAGIELVDMAGAGEANGTVVSFIKNGEEIVGFWKDDGDDEDLLECLDRCKEQYNRYRDL MISCLMNQET P48240 Exosome complex component RRP40 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.026778550999999998 1 Escherichia coli LEVO GHMSTFIFPGDSFPVDPTTPVKLGPGIYCDPNTQEIRPVNTGVLHVSAKGKSGVQTAYIDYSSKRYIPSVNDFVIGVIIG TFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIECFDSTTGRDAGFGILEDGMIIDV NLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNGKIWVKCEELSNTLACYRTIMECCQKNDTAAFKDIAKRQFKEILTVK EE Q08285 Exosome complex component RRP4 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.039714445 1 Escherichia coli LEVO RSMSEVITITKRNGAFQNSSNLSYNNTGISDDENDEEDIYMHDVNSASKSESDSQIVTPGELVTDDPIWMRGHGTYFLDN MTYSSVAGTVSRVNRLLSVIPLKGRYAPETGDHVVGRIAEVGNKRWKVDIGGKQHAVLMLGSVNLPGGILRRKSESDELQ MRSFLKEGDLLNAEVQSLFQDGSASLHTRSLKYGKLRNGMFCQVPSSLIVRAKNHTHNLPGNITVVLGVNGYIWLRKTSQ MDLARDTPSANNSSSIKSTGPTGAVSLNPSITRLEEESSWQIYSDENDPSISNNIRQAICRYANVIKALAFCEIGITQQR IVSAYEASMVYSNVGELIEKNVMESIGSDILTAEKMRGNGN P38792 Exosome complex component CSL4 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.032805644999999994 1 Escherichia coli LEVO MKHHHHHHPMACNFQFPEIAYPGKLICPQYGTENKDGEDIIFNYVPGPGTKLIQYEHNGRTLEAITATLVGTVRCEEEKK TDQEEEREGTDQSTEEEKSVDASPNDVTRRTVKNILVSVLPGTEKGRKTNKYANNDFANNLPKEGDIVLTRVTRLSLQRA NVEILAVEDKPSPIDSGIGSNGSGIVAAGGGSGAATFSVSQASSDLGETFRGIIRSQDVRSTDRDRVKVIECFKPGDIVR AQVLSLGDGTNYYLTTARNDLGVVFARAANGAGGLMYATDWQMMTSPVTGATEKRKCAKPF P53859 Exosome complex exonuclease DIS3 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.113983898 1 Escherichia coli LEVO GAMSVPAIAPRRKRLADGLSVTQKVFVRSRNGGATKIVREHYLRSDIPCLSRSCTKCPQIVVPDAQNELPKFILSDSPLE LSAPIGKHYVVLDTNVVLQAIDLLENPNCFFDVIVPQIVLDEVRNKSYPVYTRLRTLCRDSDDHKRFIVFHNEFSEHTFV ERLPNETINDRNNRAIRKTCQWYSEHLKPYDINVVLVTNDRLNREAATKEVESNIITKSLVQYIELLPNADDIRDSIPQM DSFDKDLERDTFSDFTFPEYYSTARVMGGLKNGVLYQGNIQISEYNFLEGSVSLPRFSKPVLIVGQKNLNRAFNGDQVIV ELLPQSEWKAPSSIVLDSEHFDVNDNPDIEAGDDDDNNESSSNTTVISDKQRRLLAKDAMIAQRSKKIQPTAKVVYIQRR SWRQYVGQLAPSSVDPQSSSTQNVFVILMDKCLPKVRIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVRDLGTIESAQ AETEALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPEAVSKDPLLTKRKDLRDKLICSIDPPGCVDINDALHAKK LPNGNWEVGVHIADVTHFVKPGTALDAEGAARGTSVYLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVN VNFMKSVIRSREAFSYEQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRLEAGALNLASPEVKVHMDSETSDPNEVEIK KLLATNSLVEEFMLLANISVARKIYDAFPQTAMLRRHAAPPSTNFEILNEMLNTRKNMSISLESSKALADSLDRCVDPED PYFNTLVRIMSTRCMMAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKMD MICRNINRKHRNAQFAGRASIEYYVGQVMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEY KLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPITSKRKAELLLK Q08162 3.1.13.- Exosome complex exonuclease RRP6 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.084159586
Inactive point mutant D296N
1 Escherichia coli LEVO MTSENPDVLLSRVINVVRAASSLASQDVDFYKNLDRGFSKDLKSKADKLADMANEIILSIDEHHESFELKEEDISDLWNN FGNIMDNLLEMSDHSLDKLNCAINSKSRGSDLQYLGEFSGKNFSPTKRVEKPQLKFKSPIDNSESHPFIPLLKEKPNALK PLSESLRLVDDDENNPSHYPHPYEYEIDHQEYSPEILQIREEIPSKSWDDSVPIWVDTSTELESMLEDLKNTKEIAVDLE HHDYRSYYGIVCLMQISTRERDYLVDTLKLRENLHILNEVFTNPSIVKVFHGAFMNIIWLQRDLGLYVVGLFDTYHASKA IGLPRHSLAYLLENFANFKTSKKYQLADWRIRPLSKPMTAYARADTHFLLNIYDQLRNKLIESNKLAGVLYESRNVAKRR FEYSKYRPLTPSSEVYSPIEKESPWKILMYQYNIPPEREVLVRELYQWRDLIARRDDESPRFVMPNQLLAALVAYTPTDV IGVVSLTNGVTEHVRQNAKLLANLIRDALRNIKNTNEEATPIPSSETKADGILLETISVPQIRDVMERFSVLCNSNISKS RAKPVTNSSILLGKILPREEHDIAYSKDGLPNKVKTEDIRIRAQNFKSALANLEDIIFEIEKPLVVPVKLEEIKTVDPAS APNHSPEIDNLDDLVVLKKKNIQKKQPAKEKGVTEKDAVDYSKIPNILSNKPGQNNRQQKKRRFDPSSSDSNGPRAAKKR RPAAKGKNLSFKR Q12149 3.1.13.- Exosome complex protein LRP1 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.021086296999999997 1 Escherichia coli LEVO MEDIEKIKPYVRSFSKALDELKPEIEKLTSKSLDEQLLLLSDERAKLELINRYAYVLSSLMFANMKVLGVKDMSPILGEL KRVKSYMDKAKQYDNRITKSNEKSQAEQEKAKNIISNVLDGNKNQFEPSISRSNFQGKHTKFENDELAESTTTKIIDSTD HIRKASSKKSKRLDKVGKKKGGKK P38801 ATP-dependent RNA helicase DOB1 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.12226009399999999 1 Escherichia coli LEVO MDSTDLFDVFEETPVELPTDSNGEKNADTNVGDTPDHTQDKKHGLEEEKEEHEENNSENKKIKSNKSKTEDKNKKVVVPM LADSFEQEASREVDASKGLTNSETLQVEQDGKVRLSHQVRHQVALPPNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISC IDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTE ILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTN FRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISNQIGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKM IWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLL PILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMID EKMEPQVAKGMVKGQADRLDSAFHLGYNMILNLMRVEGISPEFMLEHSFFQFQNVISVPVMEKKLAELKKDFDGIEVEDE ENVKEYHEIEQAIKGYREDVRQVVTHPANALSFLQPGRLVEISVNGKDNYGWGAVVDFAKRINKRNPSAVYTDHESYIVN VVVNTMYIDSPVNLLKPFNPTLPEGIRPAEEGEKSICAVIPITLDSIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRR FPDGIPVLDPVKNMKIEDEDFLKLMKKIDVLNTKLSSNPLTNSMRLEELYGKYSRKHDLHEDMKQLKRKISESQAVIQLD DLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQERCKEAPRLKPELA EPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVD VANTIGNSSLKEKMEAVLKLIHRDIVSAGSLYL P47047 3.6.4.13 M-phase phosphoprotein 6 homolog,M-phase phosphoprotein 6 homolog,Nuclear exosome-associated RNA binding protein,M-phase phosphoprotein 6 homolog Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.004101711
Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs to Mpp6 but the sequence is not known
1 Escherichia coli LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)PNLIISNVGYSELRKPEGVISGRKT FGDN P53725 singleParticle particle 7.5 ETHANE-PROPANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) 38.4 1 4.6 FSC 0.143 CUT-OFF 22439 PROJECTION MATCHING PROJECTION MATCHING emd_4301.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 594.0 594.0 594.0 90.0 90.0 90.0 X Y Z -0.047356263 0.11682776 0.00011799472 0.00213669 1.35 1.35 1.35 0.035 AUTHOR Structure of the nuclear RNA exosome