IntAct European Bioinformatics Institute IntAct intact http://www.ebi.ac.uk/ http://www.ebi.ac.uk/intact/query/${ac} EBI-[0-9]+|IA:[0-9]+ INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge; CB10 1SD; United Kingdom http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/ heo-2010-2 A stress-responsive system for mitochondrial protein degradation. yeast Saccharomyces cerevisiae Baker's yeast anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Heo J.M., Livnat-Levanon N., Taylor E.B., Jones K.T., Dephoure N., Ring J., Xie J., Brodsky J.L., Madeo F., Gygi S.P., Ashrafi K., Glickman M.H., Rutter J. rutter@biochem.utah. rutter@biochem.utah.edu Mol. Cell (1097-2765) 2010 Only protein-protein interactions imex curation heo-2010-1 A stress-responsive system for mitochondrial protein degradation. yeast Saccharomyces cerevisiae Baker's yeast tap tandem affinity purification TAP TAP tap sequence tag sequence tag identification sequence tag Heo J.M., Livnat-Levanon N., Taylor E.B., Jones K.T., Dephoure N., Ring J., Xie J., Brodsky J.L., Madeo F., Gygi S.P., Ashrafi K., Glickman M.H., Rutter J. rutter@biochem.utah. rutter@biochem.utah.edu Mol. Cell (1097-2765) 2010 Only protein-protein interactions imex curation heo-2010-3 A stress-responsive system for mitochondrial protein degradation. mouse-c2c12 Mouse C3H muscle myoblast c2c12 Mouse C3H muscle myoblast tap tandem affinity purification TAP TAP tap sequence tag sequence tag identification sequence tag Heo J.M., Livnat-Levanon N., Taylor E.B., Jones K.T., Dephoure N., Ring J., Xie J., Brodsky J.L., Madeo F., Gygi S.P., Ashrafi K., Glickman M.H., Rutter J. rutter@biochem.utah. rutter@biochem.utah.edu Mol. Cell (1097-2765) 2010 Only protein-protein interactions imex curation heo-2010-4 A stress-responsive system for mitochondrial protein degradation. mouse-c2c12 Mouse C3H muscle myoblast c2c12 Mouse C3H muscle myoblast tap tandem affinity purification TAP TAP tap western blot western blot Immuno blot Immuno blot Heo J.M., Livnat-Levanon N., Taylor E.B., Jones K.T., Dephoure N., Ring J., Xie J., Brodsky J.L., Madeo F., Gygi S.P., Ashrafi K., Glickman M.H., Rutter J. rutter@biochem.utah. rutter@biochem.utah.edu Mol. Cell (1097-2765) 2010 Only protein-protein interactions imex curation cdc48_yeast Cell division control protein 48 CDC48 Cell division cycle protein 48 Transitional endoplasmic reticulum ATPase homolog YDL126C protein protein yeast Saccharomyces cerevisiae Baker's yeast MGEEHKPLLDASGVDPREEDKTATAILRRKKKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVESVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSLGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEKEVKVEGEDVEMTDEGAKAEQEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFNDAPLGTTATDNANSNNSAPSGAGAAFGSNAEEDDDLYS 02ADDB9A227614D8 vms1_yeast Protein VMS1 YDR049W VMS1 VCP/CDC48-associated mitochondrial stress-responsive protein 1 protein protein yeast Saccharomyces cerevisiae Baker's yeast MNSQKASKMTGSLKKNDLYIFDLSEQLLNSLKLMSFDSTLREVEVEKTSDNDRNKESGDLQIARKKVTSNVMRCSVCQMSFDSRNEQKAHYQTDYHLMNVKRNLRGLDILSVEEFDALISKEHGIKSEDENSGGEQTSSDHEESEEASDRDPDLQTNNYMETIIENDLQKLGFQKDESDAISHINTQSPYIYFKSKYLQKNEVLAIYKSLFNKRSLSNPNEALTFWNSQENPMAISALFMVGGGHFAGAIVSHQRLNVKGNAHKKDETLIEQAVNFLEHKTFHRYTTRRKQGGSQSAMDNAKGKANSAGSALRRYNESALKTDIQGVLKDWEPYLSKCDNIFIRARNVSDKKIFTDNTVLNKGDERIKSFPFTTNRPTVLELKKAWCELSYLKILPKPEPLAVKETVQKLEVSNKKDEFKEKQEPLLEEIQTEEIISLLKKGRAPLLISFLKKNKLDGNFRLKPESKYSLTPTMLHYASQQGMKQMALILLSNIKCDPTIKNRLGRTAWDLNRNDDVRHAFQIARYNLGESFTNWDETHIGQPLSREQVDEINEKKKAIENEKAEKLIKLELEAAKEKQRFAKDAERGPGKKLTNIPSIQQQNLNSLTDEQRRRLMREQRARAAEERMKKKY 98A2007E5591A220 npl4_yeast Nuclear protein localization protein 4 NPL4 YBR170C YBR1231 HRD4 HMG-CoA reductase degradation protein 4 protein protein yeast Saccharomyces cerevisiae Baker's yeast MLIRFRSKNGTHRVSCQENDLFGTVIEKLVGNLDPNADVDTFTVCEKPGQGIHAVSELADRTVMDLGLKHGDMLILNYSDKPANEKDGVNVEIGSVGIDSKGIRQHRYGPLRIKELAVDEELEKEDGLIPRQKSKLCKHGDRGMCEYCSPLPPWDKEYHEKNKIKHISFHSYLKKLNENANKKENGSSYISPLSEPDFRINKRCHNGHEPWPRGICSKCQPSAITLQQQEFRMVDHVEFQKSEIINEFIQAWRYTGMQRFGYMYGSYSKYDNTPLGIKAVVEAIYEPPQHDEQDGLTMDVEQVKNEMLQIDRQAQEMGLSRIGLIFTDLSDAGAGDGSVFCKRHKDSFFLSSLEVIMAARHQTRHPNVSKYSEQGFFSSKFVTCVISGNLEGEIDISSYQVSTEAEALVTADMISGSTFPSMAYINDTTDERYVPEIFYMKSNEYGITVKENAKPAFPVDYLLVTLTHGFPNTDTETNSKFVSSTGFPWSNRQAMGQSQDYQELKKYLFNVASSGDFNLLHEKISNFHLLLYINSLQILSPDEWKLLIESAVKNEWEESLLKLVSSAGWQTLVMILQESG 6EF35D21338EE07E ufd1_yeast Ubiquitin fusion degradation protein 1 UFD1 PIP3 Polymerase-interacting protein 3 YGR048W protein protein yeast Saccharomyces cerevisiae Baker's yeast MFSGFSSFGGGNGFVNMPQTFEEFFRCYPIAMMNDRIRKDDANFGGKIFLPPSALSKLSMLNIRYPMLFKLTANETGRVTHGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTDVPLGQFVKLEPQSVDFLDISDPKAVLENVLRNFSTLTVDDVIEISYNGKTFKIKILEVKPESSSKSICVIETDLVTDFAPPVGYVEPDYKALKAQQDKEKKNSFGKGQVLDPSVLGQGSMSTRIDYAGIANSSRNKLSKFVGQGQNISGKAPKAEPKQDIKDMKITFDGEPAKLDLPEGQLFFGFPMVLPKEDEESAAGSKSSEQNFQGQGISLRKSNKRKTKSDHDSSKSKAPKSPEVIEID 198E0CD48B863B98 ankz1_mouse Ankyrin repeat and zinc finger domain-containing protein 1 Ankzf1 D1Ertd161e protein protein mouse Mus musculus Mouse MAKPAGDAAVGSRSGELFLPSVSSSATSPAPSAAPAPASVSLLSLNGEAPLIRGLSLVSQAPGEALAWAPRTSCPGENTSSGGKVSPYSLEISEKLFCSACDQIFQNHQEQREHYKLDWHRFNLKQRLKNKPLLSASDFEQQSSTGDLSSISGSDDTDSSSEEDLLPLDEGRAESEKPNRPPGFYPHRVLFKNAQGQFLYAYRCVLGPHQIPPEKAELLLQNLQNGGPRYYVVLMAAAGHFAGAIFQGREVVAHKTFHRYTVRAKRGTAQGLQDAHGRASRSAGANLRRYNEAMLYKDVRNLLAGPIWSKALGEAETVLFRAPRSGRSLFFGGQGAPLQRDDPRLWDIPLTTRRPTFGELQRVLHKLTTLQVYDEDPREMVRFHSPETHWKPVREERKKDTEKEKTKVPSDANKPLGQDEEPLKQGSESQEEDGSEVELELVELTLGTLDLREFEVLPKRRRRRKKKERSQEQQCGAHGPLPQQPQDEPFSQPTQEVETPLDTLVYEAKAPGQPELWDTLLAACRAGEVEVLKLQLATGLVDPGVKSLLNAPLGSGGFTLLHAAAAAGRGLVVRLLLEAGADPTVQDSRARPPYTVAADKSTRNEFRRFMEKNLDAYDYNKARVPGPLTQEMEARQATRKKEQKAARRQREQQQRKQREQEEQEQEEQRRFAALSDREKRALAAERRLAAQLGAPSPPVPDSAVASAGRCWSCGVSLQGLIPFHYLDFSFCSTRCLRDHRSQAGRPSS tera_mouse Transitional endoplasmic reticulum ATPase Vcp 15S Mg(2+)-ATPase p97 subunit Valosin-containing protein protein protein mouse Mus musculus Mouse MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFGSFRFPSGNQGGAGPSQGSGGGTGGSVYTEDNDDDLYG vms1-cdc48-3 1535498 n/a 1535502 unspecified role unspecified role prey prey c-terminal myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P25694:p.Ser565Glu mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false n/a 1535503 unspecified role unspecified role bait bait c-terminal ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false vims region required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false c-terminal sufficient to bind sufficient binding region sufficient to bind range range certain certain sequence position certain false physical association physical association false false false Fig. 4B, 4E, 5B, Supp Fig 4A vms1-npl4 1535498 n/a 1535503 unspecified role unspecified role bait bait c-terminal ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false c-terminal region sufficient to bind sufficient binding region sufficient to bind range range certain certain sequence position certain false vims region required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false n/a 1535504 unspecified role unspecified role prey prey c-terminal myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false physical association physical association false false false Fig. 4C, 4F, 5C, Supp. Fig. 4A ufd1-npl4-2 1535498 n/a 1535505 unspecified role unspecified role bait bait c-terminal ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false n/a 1535504 unspecified role unspecified role prey prey c-terminal myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false physical association physical association false false false Fig. 4D vms1-cdc48-2 1535499 n/a 1535502 unspecified role unspecified role prey prey n/a 1535503 unspecified role unspecified role bait bait c-terminal region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false physical association physical association false false false Fig. 4A ankzf1-vcp-2 1535500 n/a 1535506 unspecified role unspecified role bait bait c-terminal flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false c-terminal ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false n/a 1535507 unspecified role unspecified role prey prey physical association physical association false false false Fig. 5E ankzf1-vcp-1 1535501 n/a 1535507 unspecified role unspecified role prey prey n/a 1535506 unspecified role unspecified role bait bait c-terminal flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false c-terminal ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false Q80UU1:p.Glu685_Arg687delinsAlaAlaAla mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false Fig. 5F