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-2015-1 in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Makino DL., Schuch B., Stegmann E., Baumgärtner M., Basquin C., Conti E. DIP original experiment: DIP-265948X Nature 2015 IMEx RNA degradation paths in a 12-subunit nuclear exosome complex. Makino DL., Schuch B., Stegmann E., Baumgärtner M., Basquin C., Conti E. Only protein-protein interactions imex curation makino-2015-2 in vitro In vitro ion exchange chrom ion exchange chromatography IEC IEC ion exchange chrom predetermined predetermined participant predetermined Makino DL., Schuch B., Stegmann E., Baumgärtner M., Basquin C., Conti E. DIP original experiment: DIP-265950X Nature 2015 IMEx RNA degradation paths in a 12-subunit nuclear exosome complex. Makino DL., Schuch B., Stegmann E., Baumgärtner M., Basquin C., Conti E. Only protein-protein interactions imex curation makino-2015-3 in vitro In vitro fret fluorescent resonance energy transfer FRET RET FRET analysis FRET RET FRET analysis fret predetermined predetermined participant predetermined Makino DL., Schuch B., Stegmann E., Baumgärtner M., Basquin C., Conti E. DIP original experiment: DIP-265951X Nature 2015 IMEx RNA degradation paths in a 12-subunit nuclear exosome complex. Makino DL., Schuch B., Stegmann E., Baumgärtner M., Basquin C., Conti E. Only protein-protein interactions imex curation makino-2015-4 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., Schuch B., Stegmann E., Baumgärtner M., Basquin C., Conti E. DIP original experiment: DIP-265949X Nature 2015 IMEx RNA degradation paths in a 12-subunit nuclear exosome complex. Makino DL., Schuch B., Stegmann E., Baumgärtner M., Basquin C., Conti E. Only protein-protein interactions imex curation lrp1_yeast Exosome complex protein LRP1 LRP1 Like an rRNA processing protein 1 rRNA processing protein 47 RRP47 YC1D Yeast C1D domain-containing protein YHR081W protein protein yeast Saccharomyces cerevisiae Baker's yeast MEDIEKIKPYVRSFSKALDELKPEIEKLTSKSLDEQLLLLSDERAKLELINRYAYVLSSLMFANMKVLGVKDMSPILGELKRVKSYMDKAKQYDNRITKSNEKSQAEQEKAKNIISNVLDGNKNQFEPSISRSNFQGKHTKFENDELAESTTTKIIDSTDHIRKASSKKSKRLDKVGKKKGGKK 27D00668C296CC9A 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 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 csl4-mtr3-8 3281179 N/A 3281183 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281184 unspecified role unspecified role unspecified role unspecified role Region 122-518 Region 122-518 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 3281185 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281186 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281187 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281188 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281189 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281190 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281191 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281192 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281193 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281194 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli physical association physical association false false false csl4-mtr3-9 3281180 N/A 3281183 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281184 unspecified role unspecified role unspecified role unspecified role Region 122-518 Region 122-518 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 3281185 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281186 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281187 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281188 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281189 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281190 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281191 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281192 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281193 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281194 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli physical association physical association false false false rrp6-rrp41-1 3281181 N/A 3281184 unspecified role unspecified role fluorescence donor fluorescence donor Region 122-518 Region 122-518 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false eCFP-tag eCFP-tag cfp tag cyan fluorescent protein tag CFP cyan fluorescent protein cyan fluorescent protein CFP cfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecolx Escherichia coli N/A 3281193 unspecified role unspecified role fluorescence accept fluorescence acceptor fluorescence accept eYFP-tag eYFP-tag eyfp enhanced yellow fluorescent protein tag eyfp c-term range C-terminal range c-term range c-term range C-terminal range c-term range false ecolx Escherichia coli physical association physical association false false false csl4-mtr3-10 3281182 N/A 3281183 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281184 unspecified role unspecified role unspecified role unspecified role Region 122-518 Region 122-518 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 3281185 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281186 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281187 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281188 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281189 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281190 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281191 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281192 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281193 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3281194 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli physical association physical association false false false