DIP Database of Interacting Proteins 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ dip@mbi.ucla.edu 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ makino-2013-1 in vitro In vitro ion exchange chrom ion exchange chromatography IEC IEC ion exchange chrom predetermined predetermined participant predetermined Makino DL., Baumgärtner M., Conti E. DIP original experiment: DIP-252817X Nature 2013 IMEx Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex. Makino DL., Baumgärtner M., Conti E. Only protein-protein interactions imex curation makino-2013-2 in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Makino DL., Baumgärtner M., Conti E. DIP original experiment: DIP-252815X Nature 2013 IMEx Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex. Makino DL., Baumgärtner M., Conti E. Only protein-protein interactions imex curation makino-2013-3 in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Makino DL., Baumgärtner M., Conti E. DIP original experiment: DIP-252816X Nature 2013 IMEx Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex. Makino DL., Baumgärtner M., Conti E. Only protein-protein interactions imex curation 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 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 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 rrp6_yeast Exosome complex exonuclease RRP6 RRP6 UNC733 Ribosomal RNA-processing protein 6 YOR001W protein protein yeast Saccharomyces cerevisiae Baker's yeast MTSENPDVLLSRVINVVRAASSLASQDVDFYKNLDRGFSKDLKSKADKLADMANEIILSIDEHHESFELKEEDISDLWNNFGNIMDNLLEMSDHSLDKLNCAINSKSRGSDLQYLGEFSGKNFSPTKRVEKPQLKFKSPIDNSESHPFIPLLKEKPNALKPLSESLRLVDDDENNPSHYPHPYEYEIDHQEYSPEILQIREEIPSKSWDDSVPIWVDTSTELESMLEDLKNTKEIAVDLEHHDYRSYYGIVCLMQISTRERDYLVDTLKLRENLHILNEVFTNPSIVKVFHGAFMDIIWLQRDLGLYVVGLFDTYHASKAIGLPRHSLAYLLENFANFKTSKKYQLADWRIRPLSKPMTAYARADTHFLLNIYDQLRNKLIESNKLAGVLYESRNVAKRRFEYSKYRPLTPSSEVYSPIEKESPWKILMYQYNIPPEREVLVRELYQWRDLIARRDDESPRFVMPNQLLAALVAYTPTDVIGVVSLTNGVTEHVRQNAKLLANLIRDALRNIKNTNEEATPIPSSETKADGILLETISVPQIRDVMERFSVLCNSNISKSRAKPVTNSSILLGKILPREEHDIAYSKDGLPNKVKTEDIRIRAQNFKSALANLEDIIFEIEKPLVVPVKLEEIKTVDPASAPNHSPEIDNLDDLVVLKKKNIQKKQPAKEKGVTEKDAVDYSKIPNILSNKPGQNNRQQKKRRFDPSSSDSNGPRAAKKRRPAAKGKNLSFKR B19A0B2ED74C6DA7 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 csl4_yeast Exosome complex component CSL4 CSL4 YNL232W N1154 SKI4 CEP1 synthetic lethal protein 4 protein protein yeast Saccharomyces cerevisiae Baker's yeast MACNFQFPEIAYPGKLICPQYGTENKDGEDIIFNYVPGPGTKLIQYEHNGRTLEAITATLVGTVRCEEEKKTDQEEEREGTDQSTEEEKSVDASPNDVTRRTVKNILVSVLPGTEKGRKTNKYANNDFANNLPKEGDIVLTRVTRLSLQRANVEILAVEDKPSPIDSGIGSNGSGIVAAGGGSGAATFSVSQASSDLGETFRGIIRSQDVRSTDRDRVKVIECFKPGDIVRAQVLSLGDGTNYYLTTARNDLGVVFARAANGAGGLMYATDWQMMTSPVTGATEKRKCAKPF 52D3416EA183583B rrp4_yeast Exosome complex component RRP4 RRP4 Ribosomal RNA-processing protein 4 YHR069C protein protein yeast Saccharomyces cerevisiae Baker's yeast MSEVITITKRNGAFQNSSNLSYNNTGISDDENDEEDIYMHDVNSASKSESDSQIVTPGELVTDDPIWMRGHGTYFLDNMTYSSVAGTVSRVNRLLSVIPLKGRYAPETGDHVVGRIAEVGNKRWKVDIGGKQHAVLMLGSVNLPGGILRRKSESDELQMRSFLKEGDLLNAEVQSLFQDGSASLHTRSLKYGKLRNGMFCQVPSSLIVRAKNHTHNLPGNITVVLGVNGYIWLRKTSQMDLARDTPSANNSSSIKSTGPTGAVSLNPSITRLEEESSWQIYSDENDPSISNNIRQAICRYANVIKALAFCEIGITQQRIVSAYEASMVYSNVGELIEKNVMESIGSDILTAEKMRGNGN 0718A7ABF42E9B9B rrp40_yeast Exosome complex component RRP40 RRP40 Ribosomal RNA-processing protein 40 YOL142W protein protein yeast Saccharomyces cerevisiae Baker's yeast MSTFIFPGDSFPVDPTTPVKLGPGIYCDPNTQEIRPVNTGVLHVSAKGKSGVQTAYIDYSSKRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIECFDSTTGRDAGFGILEDGMIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNGKIWVKCEELSNTLACYRTIMECCQKNDTAAFKDIAKRQFKEILTVKEE 62B3A30348BBAA7C mtr3_yeast Exosome complex component MTR3 MTR3 YGR158C G6676 mRNA transport regulator 3 protein protein yeast Saccharomyces cerevisiae Baker's yeast MNVQDRRRLLGPAAAKPMAFSNTTTHVPEKKSTDLTPKGNESEQELSLHTGFIENCNGSALVEARSLGHQTSLITAVYGPRSIRGSFTSQGTISIQLKNGLLEKYNTNELKEVSSFLMGIFNSVVNLSRYPKSGIDIFVYLTYDKDLTNNPQDDDSQSKMMSSQISSLIPHCITSITLALADAGIELVDMAGAGEANGTVVSFIKNGEEIVGFWKDDGDDEDLLECLDRCKEQYNRYRDLMISCLMNQET 2FA07ABB4A1115E0 rrp42_yeast Exosome complex component RRP42 RRP42 Ribosomal RNA-processing protein 42 YDL111C protein protein yeast Saccharomyces cerevisiae Baker's yeast MSLSVAEKSYLYDSLASTPSIRPDGRLPHQFRPIEIFTDFLPSSNGSSRIIASDGSECIVSIKSKVVDHHVENELLQVDVDIAGQRDDALVVETITSLLNKVLKSGSGVDSSKLQLTKKYSFKIFVDVLVISSHSHPVSLISFAIYSALNSTYLPKLISAFDDLEVEELPTFHDYDMVKLDINPPLVFILAVVGNNMLLDPAANESEVANNGLIISWSNGKITSPIRSVALNDSNVKSFKPHLLKQGLAMVEKYAPDVVRSLENL 806C60979642C67E rrp46_yeast Exosome complex component RRP46 RRP46 Ribosomal RNA-processing protein 46 YGR095C protein protein yeast Saccharomyces cerevisiae Baker's yeast MSVQAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQELPTQLALEIIVRPAKGVATTREKVLEDKLRAVLTPLITRHCYPRQLCQITCQILESGEDEAEFSLRELSCCINAAFLALVDAGIALNSMCASIPIAIIKDTSDIIVDPTAEQLKISLSVHTLALEFVNGGKVVKNVLLLDSNGDFNEDQLFSLLELGEQKCQELVTNIRRIIQDNISPRLVV F1307E0EE4FC3133 csl4-mtr3-5 3250356 N/A 3250359 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250360 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250361 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250362 unspecified role unspecified role unspecified role unspecified role Region 518-693 Region 518-693 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3250363 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250364 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250365 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250366 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250367 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250368 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250369 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli association association false false false csl4-mtr3-6 3250357 N/A 3250362 unspecified role unspecified role unspecified role unspecified role Region 518-693 Region 518-693 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3250363 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250364 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250365 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250366 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250367 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250368 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250369 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250359 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250360 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250361 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli physical association physical association false false false csl4-mtr3-7 3250358 N/A 3250362 unspecified role unspecified role unspecified role unspecified role Region 518-693 Region 518-693 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3250363 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250364 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250365 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250366 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250367 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250368 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250369 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250359 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250360 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3250361 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli physical association physical association false false false