DIP Database of Interacting Proteins 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ dip@mbi.ucla.edu Visualization of distinct substrate-recruitment pathways in the yeast exosome by EM. Visualization of distinct substrate-recruitment pathways in the yeast exosome by EM. Nature structural & molecular biology 2014 imex curation Liu JJ., Bratkowski MA., Liu X., Niu CY., Ke A., Wang HW. Only protein-protein interactions in vitro In vitro tem transmission electron microscopy tem predetermined predetermined participant predetermined Liu JJ., Bratkowski MA., Liu X., Niu CY., Ke A., Wang HW. DIP original experiment: DIP-260027X Nature structural & molecular biology 2014 IMEx Visualization of distinct substrate-recruitment pathways in the yeast exosome by EM. Visualization of distinct substrate-recruitment pathways in the yeast exosome by EM. Visualization of distinct substrate-recruitment pathways in the yeast exosome by EM. Nature structural & molecular biology 2014 imex curation Liu JJ., Bratkowski MA., Liu X., Niu CY., Ke A., Wang HW. Only protein-protein interactions in vitro In vitro 3d-em 3D electron microscopy 3D-EM electron tomog predetermined predetermined participant predetermined Liu JJ., Bratkowski MA., Liu X., Niu CY., Ke A., Wang HW. DIP original experiment: DIP-260028X Nature structural & molecular biology 2014 IMEx Visualization of distinct substrate-recruitment pathways in the yeast exosome by EM. Visualization of distinct substrate-recruitment pathways in the yeast exosome by EM. Visualization of distinct substrate-recruitment pathways in the yeast exosome by EM. Nature structural & molecular biology 2014 imex curation Liu JJ., Bratkowski MA., Liu X., Niu CY., Ke A., Wang HW. Only protein-protein interactions in vitro In vitro ion exchange chrom ion exchange chromatography IEC IEC ion exchange chrom weight by comassie molecular weight estimation by coomasie staining weight by comassie Liu JJ., Bratkowski MA., Liu X., Niu CY., Ke A., Wang HW. DIP original experiment: DIP-260026X Nature structural & molecular biology 2014 IMEx Visualization of distinct substrate-recruitment pathways in the yeast exosome by EM. rrp4_yeast Exosome complex component RRP4 RRP4 Ribosomal RNA-processing protein 4 YHR069C protein protein yeast Saccharomyces cerevisiae Baker's yeast MSEVITITKRNGAFQNSSNLSYNNTGISDDENDEEDIYMHDVNSASKSESDSQIVTPGELVTDDPIWMRGHGTYFLDNMTYSSVAGTVSRVNRLLSVIPLKGRYAPETGDHVVGRIAEVGNKRWKVDIGGKQHAVLMLGSVNLPGGILRRKSESDELQMRSFLKEGDLLNAEVQSLFQDGSASLHTRSLKYGKLRNGMFCQVPSSLIVRAKNHTHNLPGNITVVLGVNGYIWLRKTSQMDLARDTPSANNSSSIKSTGPTGAVSLNPSITRLEEESSWQIYSDENDPSISNNIRQAICRYANVIKALAFCEIGITQQRIVSAYEASMVYSNVGELIEKNVMESIGSDILTAEKMRGNGN 0718A7ABF42E9B9B 0718A7ABF42E9B9B rrp41_yeast Exosome complex component SKI6 SKI6 YGR195W G7587 ECM20 Ribosomal RNA-processing protein 41 Superkiller protein 6 Extracellular mutant protein 20 RRP41 protein protein yeast Saccharomyces cerevisiae Baker's yeast MSRLEIYSPEGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNITKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTTPLLDTNSLEENAMSTVTLGVVGKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRKHAQKRVSNASAR C80EFFB528A43044 C80EFFB528A43044 rrp46_yeast Exosome complex component RRP46 RRP46 Ribosomal RNA-processing protein 46 YGR095C protein protein yeast Saccharomyces cerevisiae Baker's yeast MSVQAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQELPTQLALEIIVRPAKGVATTREKVLEDKLRAVLTPLITRHCYPRQLCQITCQILESGEDEAEFSLRELSCCINAAFLALVDAGIALNSMCASIPIAIIKDTSDIIVDPTAEQLKISLSVHTLALEFVNGGKVVKNVLLLDSNGDFNEDQLFSLLELGEQKCQELVTNIRRIIQDNISPRLVV F1307E0EE4FC3133 F1307E0EE4FC3133 rrp43_yeast Exosome complex component RRP43 RRP43 YCR035C YCR35C YCR522 Ribosomal RNA-processing protein 43 protein protein yeast Saccharomyces cerevisiae Baker's yeast MAESTTLETIEIHPITFPPEVLARISPELSLQRHLSLGIRPCLRKYEEFRDVAIENNTLSRYADAGNIDTKNNILGSNVLKSGKTIVITSITGGIIEETSAAIKDLDDFGEEELFEVTKEEDIIANYASVYPVVEVERGRVGACTDEEMTISQKLHDSILHSRILPKKALKVKAGVRSANEDGTFSVLYPDELEDDTLNETNLKMKRKWSYVLYAKIVVLSRTGPVFDLCWNSLMYALQSVKLPRAFIDERASDLRMTIRTRGRSATIRETYEIICDQTKSVPLMINAKNIAFASNYGIVELDPECQLQNSDNSEEEEVDIDMDKLNTVLIADLDTEAEETSIHSTISILAAPSGNYKQLTLVGGGAKITPEMIKRSLLLSRVRADDLSTRFNI 8801837B8184134D 8801837B8184134D rrp40_yeast Exosome complex component RRP40 RRP40 Ribosomal RNA-processing protein 40 YOL142W protein protein yeast Saccharomyces cerevisiae Baker's yeast MSTFIFPGDSFPVDPTTPVKLGPGIYCDPNTQEIRPVNTGVLHVSAKGKSGVQTAYIDYSSKRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIECFDSTTGRDAGFGILEDGMIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNGKIWVKCEELSNTLACYRTIMECCQKNDTAAFKDIAKRQFKEILTVKEE 62B3A30348BBAA7C 62B3A30348BBAA7C rrp44_yeast Exosome complex exonuclease DIS3 DIS3 Ribosomal RNA-processing protein 44 Chromosome disjunction protein 3 RRP44 O2197 YOL021C protein protein yeast Saccharomyces cerevisiae Baker's yeast MSVPAIAPRRKRLADGLSVTQKVFVRSRNGGATKIVREHYLRSDIPCLSRSCTKCPQIVVPDAQNELPKFILSDSPLELSAPIGKHYVVLDTNVVLQAIDLLENPNCFFDVIVPQIVLDEVRNKSYPVYTRLRTLCRDSDDHKRFIVFHNEFSEHTFVERLPNETINDRNDRAIRKTCQWYSEHLKPYDINVVLVTNDRLNREAATKEVESNIITKSLVQYIELLPNADDIRDSIPQMDSFDKDLERDTFSDFTFPEYYSTARVMGGLKNGVLYQGNIQISEYNFLEGSVSLPRFSKPVLIVGQKNLNRAFNGDQVIVELLPQSEWKAPSSIVLDSEHFDVNDNPDIEAGDDDDNNESSSNTTVISDKQRRLLAKDAMIAQRSKKIQPTAKVVYIQRRSWRQYVGQLAPSSVDPQSSSTQNVFVILMDKCLPKVRIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVRDLGTIESAQAETEALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPEAVSKDPLLTKRKDLRDKLICSIDPPGCVDIDDALHAKKLPNGNWEVGVHIADVTHFVKPGTALDAEGAARGTSVYLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFMKSVIRSREAFSYEQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRLEAGALNLASPEVKVHMDSETSDPNEVEIKKLLATNSLVEEFMLLANISVARKIYDAFPQTAMLRRHAAPPSTNFEILNEMLNTRKNMSISLESSKALADSLDRCVDPEDPYFNTLVRIMSTRCMMAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKMDMICRNINRKHRNAQFAGRASIEYYVGQVMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPITSKRKAELLLK 00DD31BD2D6904F4 00DD31BD2D6904F4 rrp45_yeast Exosome complex component RRP45 RRP45 YDR280W D9954.1 Ribosomal RNA-processing protein 45 protein protein yeast Saccharomyces cerevisiae Baker's yeast MAKDIEISASESKFILEALRQNYRLDGRSFDQFRDVEITFGKEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEGLFVISTEISPMAGSQFENGNITGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHGEQIIVHPVNEREPVPLGILHIPICVTFSFFNPQDTEENIKGETNSEISIIDATLKEELLRDGVLTVTLNKNREVVQVSKAGGLPMDALTLMKCCHEAYSIIEKITDQILQLLKEDSEKRNKYAAMLTSENAREI 65C9DB5A63678F2D 65C9DB5A63678F2D mtr3_yeast Exosome complex component MTR3 MTR3 YGR158C G6676 mRNA transport regulator 3 protein protein yeast Saccharomyces cerevisiae Baker's yeast MNVQDRRRLLGPAAAKPMAFSNTTTHVPEKKSTDLTPKGNESEQELSLHTGFIENCNGSALVEARSLGHQTSLITAVYGPRSIRGSFTSQGTISIQLKNGLLEKYNTNELKEVSSFLMGIFNSVVNLSRYPKSGIDIFVYLTYDKDLTNNPQDDDSQSKMMSSQISSLIPHCITSITLALADAGIELVDMAGAGEANGTVVSFIKNGEEIVGFWKDDGDDEDLLECLDRCKEQYNRYRDLMISCLMNQET 2FA07ABB4A1115E0 2FA07ABB4A1115E0 rrp42_yeast Exosome complex component RRP42 RRP42 Ribosomal RNA-processing protein 42 YDL111C protein protein yeast Saccharomyces cerevisiae Baker's yeast MSLSVAEKSYLYDSLASTPSIRPDGRLPHQFRPIEIFTDFLPSSNGSSRIIASDGSECIVSIKSKVVDHHVENELLQVDVDIAGQRDDALVVETITSLLNKVLKSGSGVDSSKLQLTKKYSFKIFVDVLVISSHSHPVSLISFAIYSALNSTYLPKLISAFDDLEVEELPTFHDYDMVKLDINPPLVFILAVVGNNMLLDPAANESEVANNGLIISWSNGKITSPIRSVALNDSNVKSFKPHLLKQGLAMVEKYAPDVVRSLENL 806C60979642C67E 806C60979642C67E mtr3-rrp4-7 3 11 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 4 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 6 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 10 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 9 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli 7 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 12 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 5 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 8 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast association association mtr3-rrp4-8 1 11 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 4 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 6 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 10 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 9 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli 7 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 12 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 5 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 8 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast physical association physical association mtr3-rrp4-9 2 11 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 4 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 6 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 10 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 9 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli 7 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 12 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 5 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 8 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast physical association physical association