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/ kimura-2009-1 An inhibitor of a deubiquitinating enzyme regulates ubiquitin homeostasis. yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Kimura Y., Yashiroda H., Kudo T., Koitabashi S., Murata S., Kakizuka A., Tanaka K. Experiment performed in a mutant strain of yeast lacking doa4 kimura-yk@igakuken.or.jp Cell (0092-8674) 2009 Only protein-protein interactions 3 imex curation kimura-2009-2 An inhibitor of a deubiquitinating enzyme regulates ubiquitin homeostasis. yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast pull down pull down anti tag western anti tag western blot anti tag western Kimura Y., Yashiroda H., Kudo T., Koitabashi S., Murata S., Kakizuka A., Tanaka K. Experiment performed in a mutant strain of yeast lacking doa4 kimura-yk@igakuken.or.jp Cell (0092-8674) 2009 Only protein-protein interactions 3 imex curation kimura-2009-3 An inhibitor of a deubiquitinating enzyme regulates ubiquitin homeostasis. yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Kimura Y., Yashiroda H., Kudo T., Koitabashi S., Murata S., Kakizuka A., Tanaka K. Experiment performed in a mutant strain of yeast lacking doa4 kimura-yk@igakuken.or.jp Cell (0092-8674) 2009 Only protein-protein interactions 3 imex curation bro1_yeast Vacuolar-sorting protein BRO1 ASI6 NPI3 VPS31 YPL084W BRO1 LPF2 BRO domain-containing protein 1 BCK1-like resistance to osmotic shock protein 1 Vacuolar protein-sorting-associated protein 31 Amino acid sensor-independent protein 6 Nitrogen permease inactivating protein 3 protein protein yeast Saccharomyces cerevisiae Baker's yeast MKPYLFDLKLKDTEKLDWKKGLSSYLKKSYGSSQWRTFYDEKATSELDHLRNNANGELAPSSLSEQNLKYYSFLEHLYFRLGSKGSRLKMDFTWYDAEYSSAQKGLKYTQHTLAFEKSCTLFNIAVIFTQIARENINEDYKNSIANLTKAFSCFEYLSENFLNSPSVDLQSENTRFLANICHAEAQELFVLKLLNDQISSKQYTLISKLSRATCNLFQKCHDFMKEIDDDVAIYGEPKWKTTVTCKLHFYKSLSAYYHGLHLEEENRVGEAIAFLDFSMQQLISSLPFKTWLVEFIDFDGFKETLEKKQKELIKDNDFIYHESVPAVVQVDSIKALDAIKSPTWEKILEPYMQDVANKCDSLYRGIIPLDVYEKESIYSEEKATLLRKQVEETETANLEYSSFIEFTNLPRLLSDLEKQFSDGNIFSNTDTQGQLMRDQIQTWCKFIQTNEFRDIEEQMNKIVFKRKQILEILSALPNDQKENVTKLKSSLVAASNSDEKLFACVKPHIVEINLLNDNGKIWKKFDEFNRNTPPQPSLLDIDDTKNDKILELLKQVKGHAEDLRTLKEERSRNLSELRDEINNDDITKLLIINKGKSDVELKDLFEVELEKFEPLSTRIEATIYKQSSMIDDIKAKLDEIFHLSNFKDKSSGEEKFLEDRKNFFDKLQEAVKSFSIFASDLPKGIEFYDSLFNMSRDLAERVRVAKQTEDSTANSPAPPLPPLDSKASVVGGPPLLPQKSAAFQSLSRQGLNLGDQFQNLKISAGSDLPQGPGIPPRTYEASPYAATPTMAAPPVPPKQSQEDMYDLRRRKAVENEERELQENPTSFYNRPSVFDENMYSKYSS ubp4_yeast Ubiquitin carboxyl-terminal hydrolase 4 DOA4 MUT4 SSV7 YDR069C YD9609.23C YD8554.02C D4270 NPI2 Ubiquitin-specific-processing protease 4 Deubiquitinating enzyme 4 Vacuole biogenesis protein SSV7 Ubiquitin thioesterase 4 DOS1 UBP4 protein protein yeast Saccharomyces cerevisiae Baker's yeast MEQNIISTIRDECIRHRSKYLTIAQLTAIAEAKINEFIITGKAKDQDLSSLLDKCIDILSIYKKNSKDIKNIISCKNKGAMISSNSVMIIQLNYVYYKVIHIIVTTNIPHLSEFAKIKLHKSTSDEGNGNNNNNEFQLMNIYNTLLETLLKDENIAKIKSFIKSSIKQTKLNHEQEECNLMRTGSYITSNQLNSLISSSANSASSQMEILLIDIRSRLEFNKSHIDTKNIICLEPISFKMSYSDHDLEKKSLITSPNSEIKMFQSRNLFKFIILYTDANEYNVKQQSVLLDILVNHSFEKPISDDFTKIFILESGFPGWLKSNYGRQVSSSFPSNNNIKDDSVYINGNTSGLSLQHLPKMSPSIRHSMDDSMKEMLVAPTPLNHLQQQQQQQSDNDHVLKRSSSFKKLFSNYTSPNPKNSNSNLYSISSLSISSSPSPLPLHSPDPVKGNSLPINYPETPHLWKNSETDFMTNQREQLNHNSFAHIAPINTKAITSPSRTATPKLQRFPQTISMNLNMNSNGHSSATSTIQPSCLSLSNNDSLDHTDVTPTSSHNYDLDFAVGLENLGNSCYMNCIIQCILGTHELTQIFLDDSYAKHININSKLGSKGILAKYFARLVHMMYKEQVDGSKKISISPIKFKLACGSVNSLFKTASQQDCQEFCQFLLDGLHEDLNQCGSNPPLKELSQEAEARREKLSLRIASSIEWERFLTTDFSVIVDLFQGQYASRLKCKVCSHTSTTYQPFTVLSIPIPKKNSRNNITIEDCFREFTKCENLEVDEQWLCPHCEKRQPSTKQLTITRLPRNLIVHLKRFDNLLNKNNDFVIYPFLLDLTPFWANDFDGVFPPGVNDDELPIRGQIPPFKYELYGVACHFGTLYGGHYTAYVKKGLKKGWLYFDDTKYKPVKNKADAINSNAYVLFYHRVYGV rfu1_yeast Regulator of free ubiquitin chains 1 RFU1 YLR073C protein protein yeast Saccharomyces cerevisiae Baker's yeast MKSSKQLVQDAKDYRFNPAIPLRIYLKTCIGILEKAQCAFQANDLSLSFIYYFRYVDLLTNKLSRHPELLRMDASSSSSSSYIHKREYLQLIKLEVPAVCKIIESLRTQIDSQYSKLQTSLANNIAKPNINANTTPVQVEQQPLPKKSFDEYSFNQSISFFQKISNAQLNTGASSQSQATARDEAYRLNYPELPRLTFST rfu1-bro1-1 Interaction between Rfu1, Ubp4 and Bro1 identified by coimmunoprecipitation 827444 n/a 827447 unspecified role unspecified role prey prey region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 827448 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 827449 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Fig. 3D rfu1-ubp4-1 Interaction between Rfu1and Ubp4 identified by coimmunoprecipitation 827445 n/a 827449 unspecified role unspecified role bait bait region mbp tag maltose binding protein tag maltose binding protein tag maltose binding protein tag mbp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast n/a 827448 unspecified role unspecified role prey prey c-terminal v5 tag v5 tag GKPIPNPLLGLDST epitope tag GKPIPNPLLGLDST epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false n-terminal flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast direct interaction direct interaction false false false Fig. 3E, Supp. Fig. 11 rfu1-bro1-2 Interaction between Rfu1 and Bro1 identified by coimmunoprecipitation 827446 n/a 827449 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 827447 unspecified role unspecified role prey prey region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Fig. 3D Interaction performed in cells lacking DOA4.