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/ ju-2008-1 Genome-wide analysis identifies MYND-domain protein Mub1 as an essential factor for Rpn4 ubiquitylation. in vitro In vitro pull down pull down anti tag western anti tag western blot anti tag western Ju D., Wang X., Xu H., Xie Y. xiey@karmanos.org Mol. Cell. Biol. (0270-7306) 2008 Only protein-protein interactions imex curation ju-2008-2 Genome-wide analysis identifies MYND-domain protein Mub1 as an essential factor for Rpn4 ubiquitylation. in vitro In vitro ubiquitinase assay ubiquitinase assay ubiquitinase assay anti tag western anti tag western blot anti tag western Ju D., Wang X., Xu H., Xie Y. xiey@karmanos.org Mol. Cell. Biol. (0270-7306) 2008 Only protein-protein interactions imex curation ju-2008-3 Genome-wide analysis identifies MYND-domain protein Mub1 as an essential factor for Rpn4 ubiquitylation. 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 Ju D., Wang X., Xu H., Xie Y. xiey@karmanos.org Mol. Cell. Biol. (0270-7306) 2008 Only protein-protein interactions imex curation rpn4_yeast Protein RPN4 RPN4 SON1 Nuclear protein SON1 Ubiquitin fusion degradation protein 5 UFD5 D2840 YDL020C protein protein yeast Saccharomyces cerevisiae Baker's yeast MASTELSLKRTLTDILEDELYHTNPGHSQFTSHYQNYHPNASITPYKLVNKNKENNTFTWNHSLQHQNESSAASIPPQQTYHFPIFNKYADPTLTTTTSFTTSEATANDRQINNVHLIPNEIKGASETPLQKTVNLKNIMKVSDPYVPTRNTFNYDVKISNDFFDNGDNLYGNDEEVLFYEDNYNPKMQWSLQDNSAAINNEDARAIFNNEFDSDDDDISDDEEDEIEENCLQQEQHQEEPLLSLDVTPISMFGSDQKTGRAKSSSHLFNEYSYVDSNMDSISSVVSEDLLDERGHEKIEDEDEDNDLDEDDIYDISLLKNRRKQSFVLNKNTIDFERFPSPSTSANVPSTATTGKRKPAKSSSNRSCVSNSNENGTLERIKKPTSAVVSSNASRRKLINYTKKHLSSHSSTNSNSKPSTASPSAHTSSSDGNNEIFTCQIMNLITNEPCGAQFSRSYDLTRHQNTIHAKRKIVFRCSECIKILGSEGYQKTFSRLDALTRHIKSKHEDLSLEQRQEVTKFAKANIGYVMG ubr2_yeast E3 ubiquitin-protein ligase UBR2 UBR2 Ubiquitin-protein ligase E3 component N-recognin-1 homolog YLR024C RING-type E3 ubiquitin transferase UBR2 protein protein yeast Saccharomyces cerevisiae Baker's yeast MEDSDLSITNIRDFLTELPKLAKCEYSETTSYLLWKTLNLRLKHSDNDINWRSLVSILNSEAWENEKYRDILNGRKWRTLEFENDHHSVGNMHIGTACTRLCFPSETIYYCFTCSTNPLYEICELCFDKEKHVNHSYVAKVVMRPEGRICHCGDPFAFNDPSDAFKCKNELNNIPISNDNSNVTDDENVISLLNYVLDFLIDVTVSYKEEAEAHSSERKASSLMHPNQNSITDDIMEKHECEPLVNDENFVFFDNNWSNTRKEAHMEWAIQIEEEECNVHYMDLASTITRILNTPVEYAISITKALEDSHDVVTVLQSENFFEIDQIAKEFQKENIVVHVRKADDIFKRKLTDDLTDWLYSLCFKAATSLQNKYALRISMLDVWYSHFSKMRVSPTNTNPDFSKINLLGGFLISNEDSDESWFKPWSLENIEDERISKILTNYNERLIRAHSPNTVSHFYNFYGSRFQYIIINSINILSKKSKFKMLKIMASLFSLRDESRKFLAAQYIDVYLSVLYDAVASDAKECQVTLMSILGQYTFQDPSIANMTISSGFIERTIRFAFTLMAFNPEDLMSYLPISLYNGFKLPTETIRNRRTIICFKDLCTIMSANTVPEELLSNEAIFNAIIESFSEFSNVLPLKRETKEHVEVENFDFSAFYFFFSSILIMTDGYTRSISLVKDAAFRKQIVLKLLDVAQTREFESLTNSRKAISPDNASTNENDSNKATLSTVRETICNYVAETINFQVGVNTQYFFNPMSYLFKFVIQWSQCGRYEPIPASLTNYINLFEVFQDKQKALYISESALSTLVLIGQINVGFWVRNGTPITHQARMYTKYSMREFTYISDIFNVQFSMAMCNPDELMVTYLSRWGLKHWANGVPMYDYPDTETTVAVVNECILLLIQLLTEVRSLVMKSSKEGFERTFKSEIIHALCFDTCSYAQIVNCIPEHITKHPSFDIYLEKYANYTSPVSLTDNGIFVLKEKYKDEIDPYYIGLSSSRRYDVEKNIRLNMANLKKMKYEDTFVPAKKVKDLLKNTLFSGLYSISSVNTFGLFLKNTLDHIIKYDYDNLLPRVVHLIHLCVVNNLNEFMGILWHEYAIVDTEFCHYHSIGSILYYCLLKDNFSESHGKIREIFRYLMETAPHVNVNSYLREQTTSYTPGILWPTKEDKSHKDKEFERKKHLARLRKKKLMKKLAQQQMKFMENNSVDTSDISTPRTTSPSLSPTRINAENSSNTINSCCDDDCVFCKMPKDDDVFVYFSYQERNICDHGIDFTNPTDVNRINSLFSGKQTKDSAIQENPQDDDGTRLKFTSCEPVLRACGHGSHTKCLSGHMKSIRGIQNQTTKNIPLSYGSGLIYCPVCNSLSNSFLPKTNDIDKRTSSQFFMCIEKRSEAEENLDPMSSICIKAAMILGDLQGKKVTTIEDAYKVVNSVFINTISNTELRLRSHKKEGKIVNMERISSQCILTLHLVCELKSFIYKKFVNSKTFSSEISRKIWNWNEFLIKGNNVNLLLYMSQNFDNIDGGKTPQPPNLCIYEMFKRRFHQLLLLLARDMMRVNFYKDCRNKIKISSNGSEEPSTSFSYLFNTFKKYVDLFKPDDVRFDFTSLEKIKDFICSLLLESLSIFCRRTFLLFNIQYDDDGDGDNNNNRSNNFMDVKQREIELIFRYFKLPNLTHFLKDFFYNELTQNIERYNDGNDNLRIQQVIYDMVQNINTRAYPSPEHIQLIELPLNLSKFSLDNDEISNKCDKYEIAVCLLCGQKCHIQKSIALQGYLQGECTDHMRNGCEITSAYGVFLMTGTNAIYLSYGKRGTFYAAPYLSKYGETNEDYKFGTPVYLNRARYANLANEIVFGNMIPHIVFRLTDGSADLGGWETM 1F60CC41EB88752F mub1_yeast MYND-type zinc finger protein MUB1 YMR100W YM6543.07 MUB1 Multi-budding protein protein protein yeast Saccharomyces cerevisiae Baker's yeast MRDSNHRSLTSNKPIVTITSTVYDRRALDINSSIPLINSLNYLTYLTSNSSKVRETVANDGALERLVSILRSCHLSLFELLDLDLENFNEHENIKDLWKEKRLALCAWKWTLTFQCLVLTGTRGTEQIRKKVVMSGVLSVLVTVLDNYLLYHKNYDFIKDQTMTFDFKGITTETMYKFMRKDENETYQQYIEFITGQDKLKLSTDKNFLNERLVAPSMTIPTDFSDIWGRFADLASNFEPDQERHDDDIDIDSEVESENFDAHKNFFSQPDINRPTISTPREFFLGRIVPKQDDVIWSLQLLAFVSKYTYMKSTLQNVELVESLSFRSMAYKIKQRISEENDLEEQERDVTVKLSSLYPYLSKNPENNSKVKALDTSKMDPFFKELEELSNRCQQEEQNEICNNHCPVLNLFERYRVPKPSDDNAYGKDKERINLRKKISDNFERRWSYDKMKKELTNIVYKNKVLTNVVNIFPLVEKYTVSAENTHDVIYWSSVIMRNSCRKNEILGVRQCANFSCGKWEDFPRQFAKCRRCKRTKYCSRKCQLKAWGYHRYWCHEVGSSHMRSTNTTTGVNTPNEPSSLNATATTAADVSNSTSTFTPNISTTVPDEISNRDENSIPE E38AA57377082966 ubc2_yeast Ubiquitin-conjugating enzyme E2 2 RAD6 UBC2 Ubiquitin-protein ligase UBC2 Ubiquitin carrier protein UBC2 Radiation sensitivity protein 6 YGL058W E2 ubiquitin-conjugating enzyme 2 protein protein yeast Saccharomyces cerevisiae Baker's yeast MSTPARRRLMRDFKRMKEDAPPGVSASPLPDNVMVWNAMIIGPADTPYEDGTFRLLLEFDEEYPNKPPHVKFLSEMFHPNVYANGEICLDILQNRWTPTYDVASILTSIQSLFNDPNPASPANVEAATLFKDHKSQYVKRVKETVEKSWEDDMDDMDDDDDDDDDDDDDEAD 5F568DC28ABBD60F uba1_yeast Ubiquitin-activating enzyme E1 1 UBA1 YKL210W protein protein yeast Saccharomyces cerevisiae Baker's yeast MSSNNSGLSAAGEIDESLYSRQLYVLGKEAMLKMQTSNVLILGLKGLGVEIAKNVVLAGVKSMTVFDPEPVQLADLSTQFFLTEKDIGQKRGDVTRAKLAELNAYVPVNVLDSLDDVTQLSQFQVVVATDTVSLEDKVKINEFCHSSGIRFISSETRGLFGNTFVDLGDEFTVLDPTGEEPRTGMVSDIEPDGTVTMLDDNRHGLEDGNFVRFSEVEGLDKLNDGTLFKVEVLGPFAFRIGSVKEYGEYKKGGIFTEVKVPRKISFKSLKQQLSNPEFVFSDFAKFDRAAQLHLGFQALHQFAVRHNGELPRTMNDEDANELIKLVTDLSVQQPEVLGEGVDVNEDLIKELSYQARGDIPGVVAFFGGLVAQEVLKACSGKFTPLKQFMYFDSLESLPDPKNFPRNEKTTQPVNSRYDNQIAVFGLDFQKKIANSKVFLVGSGAIGCEMLKNWALLGLGSGSDGYIVVTDNDSIEKSNLNRQFLFRPKDVGKNKSEVAAEAVCAMNPDLKGKINAKIDKVGPETEEIFNDSFWESLDFVTNALDNVDARTYVDRRCVFYRKPLLESGTLGTKGNTQVIIPRLTESYSSSRDPPEKSIPLCTLRSFPNKIDHTIAWAKSLFQGYFTDSAENVNMYLTQPNFVEQTLKQSGDVKGVLESISDSLSSKPHNFEDCIKWARLEFEKKFNHDIKQLLFNFPKDAKTSNGEPFWSGAKRAPTPLEFDIYNNDHFHFVVAGASLRAYNYGIKSDDSNSKPNVDEYKSVIDHMIIPEFTPNANLKIQVNDDDPDPNANAANGSDEIDQLVSSLPDPSTLAGFKLEPVDFEKDDDTNHHIEFITACSNCRAQNYFIETADRQKTKFIAGRIIPAIATTTSLVTGLVNLELYKLIDNKTDIEQYKNGFVNLALPFFGFSEPIASPKGEYNNKKYDKIWDRFDIKGDIKLSDLIEHFEKDEGLEITMLSYGVSLLYASFFPPKKLKERLNLPITQLVKLVTKKDIPAHVSTMILEICADDKEGEDVEVPFITIHL 8910804DF9156661 rpn4-ubr2-2 1480649 n/a 1480652 unspecified role unspecified role bait bait region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) n/a 1480653 unspecified role unspecified role prey prey 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 yeast Saccharomyces cerevisiae Baker's yeast physical association physical association false false false Fig. 2A rpn4-mub1 1480649 n/a 1480652 unspecified role unspecified role bait bait region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) n/a 1480654 unspecified role unspecified role prey prey purified purified 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 yeast Saccharomyces cerevisiae Baker's yeast direct interaction direct interaction false false false Fig. 4C rpn4-mub1-1 1480649 n/a 1480652 unspecified role unspecified role bait bait region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) n/a 1480654 unspecified role unspecified role prey prey n-terminal myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false region sufficient to bind sufficient binding region sufficient to bind 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 physical association physical association false false false Fig. 5C rad6-ubr2-1 1480649 n/a 1480653 unspecified role unspecified role prey prey 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 yeast Saccharomyces cerevisiae Baker's yeast n/a 1480655 unspecified role unspecified role bait bait region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) physical association physical association false false false Fig. 4B rad6-mub1-2 1480649 n/a 1480655 unspecified role unspecified role bait bait region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) n/a 1480653 unspecified role unspecified role prey prey 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 yeast Saccharomyces cerevisiae Baker's yeast n/a 1480654 unspecified role unspecified role prey prey n-terminal myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false yeast Saccharomyces cerevisiae Baker's yeast association association false false false Fig. 4B mub1-rad6 1480650 n/a 1480654 unspecified role unspecified role ancillary ancillary 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 yeast Saccharomyces cerevisiae Baker's yeast n/a 1480655 unspecified role unspecified role ancillary ancillary ecoli Escherichia coli (strain K12) n/a 1480656 unspecified role unspecified role ancillary ancillary n-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) n/a 1480652 enzyme target enzyme target substrate substrate neutral component neutral component region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) n/a 1480653 enzyme enzyme neutral component neutral component 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 yeast Saccharomyces cerevisiae Baker's yeast ubiquitination ubiquitination reaction ubiquitination false false false Fig. 3B, 3C Assay performed in presence of ATP and bovine ubiquitin. The presence of Mub1 was shown to be required for ubiquitination of RPN4 mub1-ubr2 1480651 n/a 1480654 unspecified role unspecified role prey prey n-terminal myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false n/a 1480653 unspecified role unspecified role bait bait 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 physical association physical association false false false Fig. 4A