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/ rieter-2013-1 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid predetermined predetermined participant predetermined Rieter E., Vinke F., Bakula D., Cebollero E., Ungermann C., Proikas-Cezanne T., Reggiori F. F.Reggiori@umcutrecht.nl Journal of cell science 2013 Only protein-protein interactions imex curation imex curation rieter-2013-2 in vitro In vitro affinity chrom affinity chromatography technology Affinity purification Affinity purification affinity chrom western blot western blot Immuno blot Immuno blot Rieter E., Vinke F., Bakula D., Cebollero E., Ungermann C., Proikas-Cezanne T., Reggiori F. F.Reggiori@umcutrecht.nl Journal of cell science 2013 Only protein-protein interactions imex curation imex curation rieter-2013-3 in vitro In vitro filter binding filter binding Filter overlay assay Filter overlay assay antibody detection identification by antibody antibody detection Rieter E., Vinke F., Bakula D., Cebollero E., Ungermann C., Proikas-Cezanne T., Reggiori F. F.Reggiori@umcutrecht.nl Journal of cell science 2013 Only protein-protein interactions imex curation imex curation rieter-2013-4 yeast Saccharomyces cerevisiae Baker's yeast bifc bimolecular fluorescence complementation bifc tag fluorescence tag visualisation by fluorescence tag fluorescence Rieter E., Vinke F., Bakula D., Cebollero E., Ungermann C., Proikas-Cezanne T., Reggiori F. F.Reggiori@umcutrecht.nl Journal of cell science 2013 Only protein-protein interactions imex curation imex curation atg18_yeast Autophagy-related protein 18 NMR1 YFR021W ATG18 AUT10 CVT18 SVP1 Cytoplasm to vacuole targeting protein 18 Swollen vacuole phenotype protein 1 Needed for premeiotic replication protein 1 protein protein yeast Saccharomyces cerevisiae Baker's yeast MSDSSPTINFINFNQTGTCISLGTSKGFKIFNCEPFGKFYSEDSGGYAIVEMLFSTSLLALVGIGDQPALSPRRLRIINTKKHSIICEVTFPTSILSVKMNKSRLVVLLQEQIYIYDINTMRLLHTIETNPNPRGLMAMSPSVANSYLVYPSPPKVINSEIKAHATTNNITLSVGGNTETSFKRDQQDAGHSDISDLDQYSSFTKRDDADPTSSNGGNSSIIKNGDVIVFNLETLQPTMVIEAHKGEIAAMAISFDGTLMATASDKGTIIRVFDIETGDKIYQFRRGTYATRIYSISFSEDSQYLAVTGSSKTVHIFKLGHSMSNNKLDSDDSNMEEAAADDSSLDTTSIDALSDEENPTRLAREPYVDASRKTMGRMIRYSSQKLSRRAARTLGQIFPIKVTSLLESSRHFASLKLPVETNSHVMTISSIGSPIDIDTSEYPELFETGNSASTESYHEPVMKMVPIRVVSSDGYLYNFVMDPERGGDCLILSQYSILMD 06B2DFAF842AE933 atg2_yeast Autophagy-related protein 2 Sporulation-specific protein 72 YNL242W N1106 ATG2 APG2 AUT8 SPO72 protein protein yeast Saccharomyces cerevisiae Baker's yeast MAFWLPQNIQKRLLLYVLQQISLFSNIDLSNLDVSIGSKSHFSFHDVNLSLDDLNIPNVQINEGIVDELVLKLTVSGGVEIDGSGLRFIMTPLYSSGSQELHSDFLVKSIQDLTNSMLQFSDPLTTYNRYKEDDISSSDSSSDLNSNIEASKPAANGSYTLQNMRNKALNVALAKLKIALKDVTIRFIVNDRDPSDNIVEVHLESIQLITTDANLRHINIENITISSIQKQAVPDSPVHPFNNDDLSQSVYLSKMEATSLYMSAMEEQSNEDPSEPQVTQEEQENDKCKESLMEINNLNIAFKGLSSVNDLRMSNIVIDIQDVHLAIHKIVEIKNSTLKNIIDIIVTHLDANESFSCQDSQSPSPDKQEPSALSSVDIKCIYLNLGQDITVILKSFKLEQKENNSLAFSLGSFYSNSSPLTISHKTKPLLTGEQTPQSIALNMGDELDIIISHDGIAHFFKIFQFVSKCMSFYQNKSKGMMPQIASDTKRTVQLTSKAVKLSLKFPYFLLCFQVSPFIYDSNRELYIELVDVFKKLPSRCTKILTMSSITISNLQSPLQLGSYDDTLKEALIYSSVHAIIKEVIFNEEYSGIVQLVEDISAFGKLFTDSKNSECTGKSKSKRGSFLQRSVRVLNSSRFVYKQSLSANFSLKIDSMKLKVSEIIGPQFGSVEALLSNNFFAITDDSQIVYFTKNLKVERKTPSLLEPQEIMSVVLNKAVNEPVLYVHRRANGKLKVIFNNIRIHYYARWLEILKKNIGPDNASSKDEPVSQKLSKKQPTSGFPWELKCLDCSLILHPFRLKSVMVIVLDNLTTGGSSFIPQAKLLSKANTLFLIDDYQNFKIQKDKNWPSLINFYAGQGFSAIGKIDTLNFLINKSDGALLLDCKIEQVGLSLCADSFQTFCQLCIDLKYPQTFPDEEKFRTQLKNPIDVFKDIDCDLFNSAFIRENNHQNDYDSVHLVDSFLDKTHEFNNGARSKLSSQGSYEMDSSSGTATGGILLPHESYLDSAQPKEEDTPPIASKEQERDVDIRGSIDVEKVVIKLFDGYDWKYTRKFIANTVEKLDKELSKAEASSSKSNVPQSEANIFDSIYISANKNNVTDLRRNLDGEIQGVQNSFSDVSKVNLRPSKHYKALIQLNKVHVNLKNYRVDEPDESNSDNSTDVLNRCVVSIYEFEIIDNVPTSTWNKFVTLLKHEPWPHSSPMFLLDLEFIRPIDFLQAVELVMQLNVAPLRLHVDQDTLEFLIRFLGFKDKRFELIDEYPDIVFIQKFSTNSIKLRLDYKPKKVDYAGLRSGQTSELMNFFTLDGSKIILKSVVLYGLNGFDELNNKLKAIWTPDITKKQLPGVLEGLAPVRSFMAIGSGVKTLVTVLMSEYRQEGHLGRSLKKGGNVFLKTTTGDFVKLGVKLTSGTQAILENTEELFGGVGSNGRVYDASKFGSADGADSDTAAVLDLDTLFEEDQLVGSKYSRIRDHEPTAVVIDMSSPGDHNEPTIVSLYADQPLDLPTGLKEAYSSLEKHMHIAYDAVWRAKGQMKDDKRGGPSAAAVYVARAAPVAIIRPLIGATEAVSKTLQGIANQVDKTHNEQINDKYKSNRTDS 54FDDF56297FFF99 1-phosphatidyl-1d-myo-inositol 3,5-bisphosphate 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphates small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) atg18-atg2-8 1931457 N/A 1931461 unspecified role unspecified role prey prey loop1, loop2 required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false P43601:p.[Glu42_Ser44delinsAlaAlaAla;Tyr47Ala;Thr90_Ser94delinsAlaAlaAlaAlaAla] mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false N/A 1931462 unspecified role unspecified role bait bait physical association physical association false false false Fig. 1 atg2-atg18-1 1931458 N/A 1931461 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 P43601:p.Thr90_Ser94delinsAlaAlaAlaAlaAla mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false region required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false P43601:p.[Glu42_Ser44delinsAlaAlaAla;Tyr47Ala;Thr90_Ser94delinsAlaAlaAlaAlaAla] mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false yeast Saccharomyces cerevisiae Baker's yeast N/A 1931462 unspecified role unspecified role bait bait c-terminal protein a tag protein a tag protein A protein A c-term range C-terminal range c-term range c-term range C-terminal range c-term range false yeast Saccharomyces cerevisiae Baker's yeast physical association physical association false false false Fig. 2A, 7E Interaction was not observed in ATG14-/- cells, which the authors interpreted as indicating that the interaction requires the generation of PtDIns3P. phosphatidylethanolamine-atg18-1 1931459 N/A 1931461 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 P43601:p.Arg285_Arg286delinsAlaAla mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false yeast Saccharomyces cerevisiae Baker's yeast N/A 1931463 unspecified role unspecified role bait bait physical association physical association false false false Fig. 2B atg2-atg18-2 1931460 N/A 1931461 unspecified role unspecified role neutral component neutral component c-terminal venus-c venus c-terminal fragment c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P43601:p.Thr90_Ser94delinsAlaAlaAlaAlaAla mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false P43601:p.Arg285_Arg286delinsAlaAla mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false N/A 1931462 unspecified role unspecified role neutral component neutral component c-terminal venus-n venus n-terminal fragment n-term range n-terminal range n-term range n-term range n-terminal range n-term range false physical association physical association false false false Fig. 7A-D Interaction increased in atg3-/- cells, and was complete lost in atg13-/- cells.