DIP Database of Interacting Proteins 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ dip@mbi.ucla.edu Structure of the Cdc48 segregase in the act of unfolding an authentic substrate. Structure of the Cdc48 segregase in the act of unfolding an authentic substrate. Science (New York, N.Y.) 2019 imex curation Cooney I., Han H., Stewart MG., Carson RH., Hansen DT., Iwasa JH., Price JC., Hill CP., Shen PS. chris@biochem.utah.edu, peter.shen@biochem.utah.edu 28-Sep-2020: Contacted by IntAct-Help. Only protein-protein interactions imex curation yeast Saccharomyces cerevisiae Baker's yeast 3d-em 3D electron microscopy 3D-EM electron tomog structure determination identification by structure determination identification by structure determination structure determination Cooney I., Han H., Stewart MG., Carson RH., Hansen DT., Iwasa JH., Price JC., Hill CP., Shen PS. chris@biochem.utah.edu, peter.shen@biochem.utah.edu Accepted 2020-JUL-17 AT 10:49 BST AT 10:49 BST by LUANA Science (New York, N.Y.) 2019 Only protein-protein interactions imex curation imex curation Structure of the Cdc48 segregase in the act of unfolding an authentic substrate. Structure of the Cdc48 segregase in the act of unfolding an authentic substrate. Science (New York, N.Y.) 2019 imex curation Cooney I., Han H., Stewart MG., Carson RH., Hansen DT., Iwasa JH., Price JC., Hill CP., Shen PS. chris@biochem.utah.edu, peter.shen@biochem.utah.edu 28-Sep-2020: Contacted by IntAct-Help. Only protein-protein interactions imex curation yeast Saccharomyces cerevisiae Baker's yeast coip coimmunoprecipitation co-immunoprecipitation CoIp immunoprecipitation Co-IP co-immunoprecipitation CoIp immunoprecipitation Co-IP coip mudpit multidimensional protein identification technology mudpit Cooney I., Han H., Stewart MG., Carson RH., Hansen DT., Iwasa JH., Price JC., Hill CP., Shen PS. chris@biochem.utah.edu, peter.shen@biochem.utah.edu Accepted 2020-JUL-17 AT 10:49 BST AT 10:49 BST by LUANA Science (New York, N.Y.) 2019 Only protein-protein interactions imex curation imex curation oat_yeast Ornithine aminotransferase CAR2 CARGB YLR438W L9753.2 Ornithine--oxo-acid aminotransferase protein protein yeast Saccharomyces cerevisiae Baker's yeast MSEATLSSKQTIEWENKYSAHNYHPLPVVFHKAKGAHVWDPEGKLYLDFLSAYSAVNQGHCHPHIIKALTEQAQTLTLSSRAFHNDVYAQFAKFVTEFFGFETVLPMNTGAEAVETALKLARRWGYMKKNIPQDKAIILGAEGNFHGRTFGAISLSTDYEDSKLHFGPFVPNVASGHSVHKIRYGHAEDFVPILESPEGKNVAAIILEPIQGEAGIVVPPADYFPKVSALCRKHNVLLIVDEIQTGIGRTGELLCYDHYKAEAKPDIVLLGKALSGGVLPVSCVLSSHDIMSCFTPGSHGSTFGGNPLASRVAIAALEVIRDEKLCQRAAQLGSSFIAQLKALQAKSNGIISEVRGMGLLTAIVIDPSKANGKTAWDLCLLMKDHGLLAKPTHDHIIRLAPPLVISEEDLQTGVETIAKCIDLL A0B6BE492FC5C1B8 A0B6BE492FC5C1B8 cdc53_yeast Cell division control protein 53 CDC53 YDL132W D2190 Cullin-A E3 ubiquitin ligase complex SCF subunit CDC53 protein protein yeast Saccharomyces cerevisiae Baker's yeast MSETLPRSDDLEATWNFIEPGINQILGNEKNQASTSKRVYKILSPTMYMEVYTAIYNYCVNKSRSSGHFSTDSRTGQSTILVGSEIYEKLKNYLKNYILNFKQSNSETFLQFYVKRWKRFTIGAIFLNHAFDYMNRYWVQKERSDGKRHIFDVNTLCLMTWKEVMFDPSKDVLINELLDQVTLGREGQIIQRSNISTAIKSLVALGIDPQDLKKLNLNVYIQVFEKPFLKKTQEYYTQYTNDYLEKHSVTEYIFEAHEIIKREEKAMTIYWDDHTKKPLSMALNKVLITDHIEKLENEFVVLLDARDIEKITSLYALIRRDFTLIPRMASVFENYVKKTGENEISSLLAMHKHNIMKNENANPKKLALMTAHSLSPKDYIKKLLEVHDIFSKIFNESFPDDIPLAKALDNACGAFININEFALPAGSPKSATSKTSEMLAKYSDILLKKATKPEVASDMSDEDIITIFKYLTDKDAFETHYRRLFAKRLIHGTSTSAEDEENIIQRLQAANSMEYTGKITKMFQDIRLSKILEDDFAVALKNEPDYSKAKYPDLQPFVLAENMWPFSYQEVEFKLPKELVPSHEKLKESYSQKHNGRILKWLWPLCRGELKADIGKPGRMPFNFTVTLFQMAILLLYNDADVLTLENIQEGTSLTIQHIAAAMVPFIKFKLIQQVPPGLDALVKPETQFKLSRPYKALKTNINFASGVKNDILQSLSGGGHDNHGNKLGNKRLTEDERIEKELNTERQIFLEACIVRIMKAKRNLPHTTLVNECIAQSHQRFNAKVSMVKRAIDSLIQKGYLQRGDDGESYAYLA 22BC8B35034EDDEF 22BC8B35034EDDEF vms1_yeast Protein VMS1 YDR049W VMS1 VCP/CDC48-associated mitochondrial stress-responsive protein 1 protein protein yeast Saccharomyces cerevisiae Baker's yeast MNSQKASKMTGSLKKNDLYIFDLSEQLLNSLKLMSFDSTLREVEVEKTSDNDRNKESGDLQIARKKVTSNVMRCSVCQMSFDSRNEQKAHYQTDYHLMNVKRNLRGLDILSVEEFDALISKEHGIKSEDENSGGEQTSSDHEESEEASDRDPDLQTNNYMETIIENDLQKLGFQKDESDAISHINTQSPYIYFKSKYLQKNEVLAIYKSLFNKRSLSNPNEALTFWNSQENPMAISALFMVGGGHFAGAIVSHQRLNVKGNAHKKDETLIEQAVNFLEHKTFHRYTTRRKQGGSQSAMDNAKGKANSAGSALRRYNESALKTDIQGVLKDWEPYLSKCDNIFIRARNVSDKKIFTDNTVLNKGDERIKSFPFTTNRPTVLELKKAWCELSYLKILPKPEPLAVKETVQKLEVSNKKDEFKEKQEPLLEEIQTEEIISLLKKGRAPLLISFLKKNKLDGNFRLKPESKYSLTPTMLHYASQQGMKQMALILLSNIKCDPTIKNRLGRTAWDLNRNDDVRHAFQIARYNLGESFTNWDETHIGQPLSREQVDEINEKKKAIENEKAEKLIKLELEAAKEKQRFAKDAERGPGKKLTNIPSIQQQNLNSLTDEQRRRLMREQRARAAEERMKKKY 98A2007E5591A220 98A2007E5591A220 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 02ADDB9A227614D8 ppz1_yeast Serine/threonine-protein phosphatase PP-Z1 PPZ1 YM9571.02C YML016C protein protein yeast Saccharomyces cerevisiae Baker's yeast MGNSSSKSSKKDSHSNSSSRNPRPQVSRTETSHSVKSAKSNKSSRSRRSLPSSSTTNTNSNVPDPSTPSKPNLEVNHQRHSSHTNRYHFPSSSHSHSNSQNELLTTPSSSSTKRPSTSRRSSYNTKAAADLPPSMIQMEPKSPILKTNNSSTHVSKHKSSYSSTYYENALTDDDNDDKDNDISHTKRFSRSSNSRPSSIRSGSVSRRKSDVTHEEPNNGSYSSNNQENYLVQALTRSNSHASSLHSRKSSFGSDGNTAYSTPLNSPGLSKLTDHSGEYFTSNSTSSLNHHSSRDIYPSKHISNDDDIENSSQLSNIHASMENVNDKNNNITDSKKDPNEEFNDIMQSSGNKNAPKKFKKPIDIDETIQKLLDAGYAAKRTKNVCLKNNEILQICIKAREIFLSQPSLLELSPPVKIVGDVHGQYGDLLRLFTKCGFPPSSNYLFLGDYVDRGKQSLETILLLFCYKIKYPENFFLLRGNHECANVTRVYGFYDECKRRCNIKIWKTFIDTFNTLPLAAIVAGKIFCVHGGLSPVLNSMDEIRHVVRPTDVPDFGLINDLLWSDPTDSPNEWEDNERGVSYCYNKVAINKFLNKFGFDLVCRAHMVVEDGYEFFNDRSLVTVFSAPNYCGEFDNWGAVMSVSEGLLCSFELLDPLDSAALKQVMKKGRQERKLANQQQQMMETSITNDNESQQ 8B7F009521F72C15 8B7F009521F72C15 odp2_yeast Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial LAT1 ODP2 YNL071W N2374 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex Pyruvate dehydrogenase complex component E2 PDA2 protein protein yeast Saccharomyces cerevisiae Baker's yeast MSAFVRVVPRISRSSVLTRSLRLQLRCYASYPEHTIIGMPALSPTMTQGNLAAWTKKEGDQLSPGEVIAEIETDKAQMDFEFQEDGYLAKILVPEGTKDIPVNKPIAVYVEDKADVPAFKDFKLEDSGSDSKTSTKAQPAEPQAEKKQEAPAEETKTSAPEAKKSDVAAPQGRIFASPLAKTIALEKGISLKDVHGTGPRGRITKADIESYLEKSSKQSSQTSGAAAATPAAATSSTTAGSAPSPSSTASYEDVPISTMRSIIGERLLQSTQGIPSYIVSSKISISKLLKLRQSLNATANDKYKLSINDLLVKAITVAAKRVPDANAYWLPNENVIRKFKNVDVSVAVATPTGLLTPIVKNCEAKGLSQISNEIKELVKRARINKLAPEEFQGGTICISNMGMNNAVNMFTSIINPPQSTILAIATVERVAVEDAAAENGFSFDNQVTITGTFDHRTIDGAKGAEFMKELKTVIENPLEMLL 49D64C738926E784 49D64C738926E784 ubx7_yeast UBX domain-containing protein 7 YBR1741 YBR273C UBX7 protein protein yeast Saccharomyces cerevisiae Baker's yeast MLEALFRDSVEEAINDSIKEGVVLAVYNTARDDQWLKSWFKGDDVSLDTLAEHSIWLRLVKDTEQFQLFEQVFPNVVVPSIYLIRAGKIELIIQGEDDRHWEKLLACIGIKDKKAGESSSRETNPGLAREEKSSRDVHRKNARERIAETTLEIQRREQLKQRKLAEEERERIIRLVRADRAERKALDETHHRTLDDDKPLDVHDYIKDAQKLHSSKCVLQIRMTDGKTLKHEFNSSETLNDVRKWVDVNRTDGDCPYSFHRGIPRVTFKDSDELKTLETLELTPRSALLLKPLETQNSGLSVTGMEGPSLLGRLYKGFSTWWHNDKDPEVTSQREETSKPNRHEVRSSTPLSGAASSSCFQYNNVREPVQSSAHASPMLTPSGTRYPSETNLTTSRSVSPNVFQFVNNDHQEDPEDPTTFNGNNVHLEKKKDEDKK 2E47ADF0E5E06797 ubx4_yeast UBX domain-containing protein 4 UBX4 YM9916.06C YMR067C protein protein yeast Saccharomyces cerevisiae Baker's yeast MPMVTVKYNFQLFKCKVSLNSTLNDVLHQSIQFFQLHTSSNDWSLIHLDKPVPLDLPWRLLNLPTGVNLELSKSSNFPVANKTNREDIPFNTIKIRFQIPGRDSVVKEMPSDQPIAPILRQMSGAAGDDFKIQVFSKIIEFKTIKDENLTLENLGIQEPSSVRLIFNNTSHSEGISANSAIHPKQTPPTMTNPETVASLPPHELHKPSVFLPSDEPLAVIKDQIEDEEDYELTVEQAKKYQKMLSSKAGTLGGPILTKRLREQSANNLPKKNKAISECLLRVKFPDRSHIQIAFKPNEDMRTVYNVVSQFLIDENMPFTLNQSHPFKPLAKDDKKLLDDLEFGSKTMLLFETNSNSNGPLIKAHLLEDAQKITHETRTTPSVNTINKSNPQGPSDNATSIKKTLNRVPKWMKLSKK 615E5F8EC1DCDD31 ufd2_yeast E4 ubiquitin-protein ligase UFD2 UFD2 YDL190C D1255 Ubiquitin fusion degradation protein 2 Ubiquitin conjugation factor E4 RING-type E3 ubiquitin transferase UFD2 protein protein yeast Saccharomyces cerevisiae Baker's yeast MTAIEDILQITTDPSDTRGYSLLKSEEVPQGSTLGVDFIDTLLLYQLTENEKLDKPFEYLNDCFRRNQQQKRITKNKPNAESLHSTFQEIDRLVIGYGVVALQIENFCMNGAFINYITGIVSNVNSYTDFLSQIIQRAILEGTALDLLNAVFPTLLEYCNKHVSHFDLNESVIYNNVLTIFELFVTFKPIAEIFTKIDGFFADYSCKPQDFERKTILGPILSLSPIEAAVAIRNYGDNLLRSKQQTAMIHESLQAEHKVVIDRLFFIVDKLVRGSLNSRTDMISYFAHIANKNHLRRADHPPFKELSSNGFMSNITLLLVRFSQPFLDISYKKIDKIDANYFNNPSLFIDLSGETRLNSDFKEADAFYDKNRKTADSKPNFISDCFFLTLTYLHYGLGGTLSFEEKMGSEIKALKEEIEKVKKIAANHDVFARFITAQLSKMEKALKTTESLRFALQGFFAHRSLQLEVFDFICGASTFLIRVVDPEHEFPFKQIKLPLIPDQIGVENVDNADFLRAHAPVPFKYYPEFVVEGPVNYSLYISKYQTSPIFRNPRLGSFVEFTTMVLRCPELVSNPHLKGKLVQLLSVGAMPLTDNSPGFMMDIFEHDELVNKNLLYALLDFYVIVEKTGSSSQFYDKFNSRYSISIILEELYYKIPSYKNQLIWQSQNNADFFVRFVARMLNDLTFLLDEGLSNLAEVHNIQNELDNRARGAPPTREEEDKELQTRLASASRQAKSSCGLADKSMKLFEIYSKDIPAAFVTPEIVYRLASMLNYNLESLVGPKCGELKVKDPQSYSFNPKDLLKALTTVYINLSEQSEFISAVAKDERSFNRNLFVRAVDILGRKTGLASPEFIEKLLNFANKAEEQRKADEEEDLEYGDVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDVTPNEELRQKILCFKKQKKEEAKHKASE 877ACB59AC29634A 877ACB59AC29634A ppz2_yeast Serine/threonine-protein phosphatase PP-Z2 PPZ2 D9461.22 YDR436W protein protein yeast Saccharomyces cerevisiae Baker's yeast MGNSGSKQHTKHNSKKDDHDGDRKKTLDLPPLTKSDTTHSLKSSRSLRSLRSKRSEASLASNVQAQTQPLSRRSSTLGNGNRNHRRSNNAPITPPNNHYLTSHPSSSRRLSSSSRRSSMGNNNNSELPPSMIQMEPKSPILKNSTSMHSTSSFNSYENALTDDDDDRGDDGGESPSMAKVTRINTSSSADRGSKRTPLRRHNSLQPEKGVTGFSSTSSKLRRRSDNTLPASYPLNAEAGGNGSDYFSNRSNSHASSRKSSFGSTGNTAYSTPLHSPALRKMSSRDNDDSGDNVNGRGTSPIPNLNIDKPSPSASSASKREYLSAYPTLAHRDSSSSLSPRGKGQRSSSSSSSSQRIYVSPPSPTGDFVHGSCADGDNGSRTNTMVEMKRKKPVRPVDIDEIIQRLLDAGYAAKRTKNVCLKNSEIIQICHKARELFLAQPALLELSPSVKIVGDVHGQYADLLRLFTKCGFPPMANYLFLGDYVDRGKQSLETILLLLCYKIKYPENFFLLRGNHECANVTRVYGFYDECKRRCNIKIWKTFVDTFNTLPLAAIVTGKIFCVHGGLSPVLNSMDEIRHVSRPTDVPDFGLINDLLWSDPTDSSNEWEDNERGVSFCYNKVAINKFLNKFGFDLVCRAHMVVEDGYEFFNDRSLVTVFSAPNYCGEFDNWGAVMTVSEGLLCSFELLDPLDSTALKQVMKKGRQERKLANR 3095F37046489AFB 3095F37046489AFB doa1_yeast Protein DOA1 YKL213C DOA1 UFD3 ZZZ4 Degradation of alpha protein 1 Ubiquitin fusion degradation protein 3 protein protein yeast Saccharomyces cerevisiae Baker's yeast MGYQLSATLKGHDQDVRDVVAVDDSKVASVSRDGTVRLWSKDDQWLGTVVYTGQGFLNSVCYDSEKELLLFGGKDTMINGVPLFATSGEDPLYTLIGHQGNVCSLSFQDGVVISGSWDKTAKVWKEGSLVYNLQAHNASVWDAKVVSFSENKFLTASADKTIKLWQNDKVIKTFSGIHNDVVRHLAVVDDGHFISCSNDGLIKLVDMHTGDVLRTYEGHESFVYCIKLLPNGDIVSCGEDRTVRIWSKENGSLKQVITLPAISIWSVDCMSNGDIIVGSSDNLVRIFSQEKSRWASEDEINELSTQVEKSTISSKTIEFDESKLSPYEILQSPGRKEGQIVVVKSPQGTIEAHQFSNSSWKKVGDVVGAGATGNDKKIEFEGKTYDYVFDVDIEDGKPPLKLPINVSDNPYTAADNFLARYELPMSYRDQVVQFILKNTNGISLDQPNDNASSSAVSPSKTSVMKVLPVKQYLIMENYNPDTIFNGIVKINSNEKTFDDEILAQIGGALHDIDESWELLLSFANTIRSNWEIKTPAYDIVRLIVKKLPYSSDIKDYIEEGLGNKNITLTMLTVRILVNCFNNENWGVKLLESNQVYKSIFETIDTEFSQASAKQSQNLAIAVSTLIFNYSALVTKGNSDLELLPIVADAINTKYGPLEEYQECEEAAYRLTVAYGNLATVEPTLRQFANSVTWLANIKRSYGNVPRFKDIFDDLS 593B808169283B5F 593B808169283B5F ppq1_yeast Serine/threonine-protein phosphatase PPQ PPQ1 SAL6 YPL179W protein protein yeast Saccharomyces cerevisiae Baker's yeast MRRSPSRSNNNFAVPNCSTNSNSSQQQLTTPSDDLNSNEPNDPDDSRSLPTIKKFNNKHSINNYNTLASAGKNNNNKRASNDNLLIPGENAHKQKIYTKDENLKSLYLDIDVSVAKALSSSATAPKLINTARTSSTTTATTSNNILTSPSYRESNYSSPSSYSFSSYYSSATSASSSTSSFLKSSGLSSRVKSPSSSVKAGSFGAPSSPTSGIPNPKSSKKPIFLRRYSHDTSSNEGLDIDVAIEKLLQVGESREITKTSKKKNFPFHSWEIQLICYHAREIFLNQPTLLRLQAPIKVVGDVHGQFNDLLRILKLSGVPSDTNYLFLGDYVDRGKNSLETILLLLCYKIKYKDNFFMLRGNHESANVTKMYGFYDECKRRLSSKVWKMFVDVFNTLPLAAIIQDKIFCVHGGISPDLHDMKQIEKVARPTDIPESGLVTDLLWSDPDPQVTDWSENDRGVSYTFSKRNVLDFCAKFKFDLILRGHMVVEDGYEFFARKKFVTIFSAPNYCGEFHNWGAVMSVTTGMMCSFELLKPRALKNKKKLYKTKV 1E26D05E2865A8C1 1E26D05E2865A8C1 pp12_yeast Serine/threonine-protein phosphatase PP1-2 GLC7 CID1 DIS2 YER133W protein protein yeast Saccharomyces cerevisiae Baker's yeast MDSQPVDVDNIIDRLLEVRGSKPGQQVDLEENEIRYLCSKARSIFIKQPILLELEAPIKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFILRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIIDEKIFCMHGGLSPDLNSMEQIRRVMRPTDIPDVGLLCDLLWSDPDKDIVGWSENDRGVSFTFGPDVVNRFLQKQDMELICRAHQVVEDGYEFFSKRQLVTLFSAPNYCGEFDNAGAMMSVDESLLCSFQILKPAQKSLPRQAGGRKKK 71B20E3A4ED93235 71B20E3A4ED93235 ypi1_yeast Type 1 phosphatases regulator YPI1 YFR003C YPI1 protein protein yeast Saccharomyces cerevisiae Baker's yeast MSGNQMAMGSEQQQTVGSRTVSVEEVPAVLQLRATQDPPRSQEAMPTRHNVRWEENVIDNENMNKKKTKICCIFHPQNEDEEECNHHSDDDGSSSSGSSSSESENEKDLDFNERRQRRLERRHRKLEKKRSYSPNAYEIQPDYSEYRRKQQEKKD E191184DCD5EF8A1 E191184DCD5EF8A1 sds22_yeast Protein phosphatase 1 regulatory subunit SDS22 YKL193C SDS22 EGP1 protein protein yeast Saccharomyces cerevisiae Baker's yeast MDKNSVNKDSEEKDERHKIEVVDDTNPDFITADSELTQDLPDDVEVIDLVHLKIKSLEDLNLYRFKNLKQLCLRQNLIESISEVEVLPHDKIVDLDFYDNKIKHISSNVNKLTKLTSLDLSFNKIKHIKNLENLTDLENLYFVQNSISKIENLSTLKSLKNLELGGNKVHSIEPDSFEGLSNLEEIWLGKNSIPRLINLHPLKNLKILSIQSNKLKKIENLEELTNLEELYLSHNFITKIEGLEKNLKLTTLDVTSNKITSLENLNHLSNLTDIWASFNKIDQSFESLGENLSALSRLETIYLEGNPIQLENKTSYRRKLTMNLPPSLQKIDATYIRG 1EF434C7276ABAEA 1EF434C7276ABAEA ubx1_yeast UBX domain-containing protein 1 SHP1 YBL058W YBL0509 YBL0515 UBX1 Suppressor of high-copy PP1 protein protein protein yeast Saccharomyces cerevisiae Baker's yeast MAEIPDETIQQFMALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQKDRREEAHWNRQQEKALKQEAFSTNSSNKAINTEHVGGLCPKPGSSQGSNEYLKRKGSTSPEPTKGSSRSGSGNNSRFMSFSDMVRGQADDDDEDQPRNTFAGGETSGLEVTDPSDPNSLLKDLLEKARRGGQMGAENGFRDDEDHEMGANRFTGRGFRLGSTIDAADEVVEDNTSQSQRRPEKVTREITFWKEGFQVADGPLYRYDDPANSFYLSELNQGRAPLKLLDVQFGQEVEVNVYKKLDESYKAPTRKLGGFSGQGQRLGSPIPGESSPAEVPKNETPAAQEQPMPDNEPKQGDTSIQIRYANGKREVLHCNSTDTVKFLYEHVTSNANTDPSRNFTLNYAFPIKPISNDETTLKDADLLNSVVVQRWA AB46C88D7ED4F11C AB46C88D7ED4F11C ubp2_yeast Ubiquitin carboxyl-terminal hydrolase 2 UBP2 YOR124C O3281 YOR3281C Ubiquitin-specific-processing protease 2 Deubiquitinating enzyme 2 Ubiquitin thioesterase 2 protein protein yeast Saccharomyces cerevisiae Baker's yeast MPNEDNELQKAIENHHNQLLNQDKENADRNGSVIEDLPLYGTSINQQSTPGDVDDGKHLLYPDIATNLPLKTSDRLLDDILCDTIFLNSTDPKVMQKGLQSRGILKESMLSYSTFRSSIRPNCLGSLTDQVVFQTKSEYDSISCPKYNKIHVFQAVIFNPSLAEQQISTFDDIVKIPIYHLKVSVKVRQELERLKKHVGVTQFHSLDHLHEYDRVDLSTFDSSDPNLLDYGIYVSDDTNKLILIEIFKPEFNSPEEHESFTADAIKKRYNAMCVKNESLDKSETPSQVDCFYTLFKIFKGPLTRKSKAEPTKTIDSGNLALNTHLNPEWLTSKYGFQASSEIDEETNEIFTEYVPPDMVDYVNDLETRKIRESFVRKCLQLIFWGQLSTSLLAPNSPLKNTKSVKGMSSLQTSFSTLPWFHLLGESRARILLNSNEQTHSPLDAEPHFINLSVSHYYTDRDIIRNYESLSSLDPENIGLYFDALTYIANRKGAYQLIAYCGKQDIIGQEALENALLMFKINPKECNISELNEATLLSIYKYETSNKSQVTSNHLTNLKNALRLLAKYTKSDKLKFYVDHEPYRALSQAYDTLSIDESVDEDIIKTAYSVKINDSPGLKLDCDRALYTIAISKRSLDLFNFLTEECPQFSNYYGPEKLDYQEALKLLQVNENASDETILKIFKQKWFDENVYEPDQFLILRAALTKISIERNSTLITNFLLTGTIDPNSLPPENWPTGINNIGNTCYLNSLLQYYFSIAPLRRYVLEYQKTVENFNDHLSNSGHIRRIGGREISRGEVERSIQFIYQLRNLFYAMVHTRERCVTPSKELAYLAFAPSNVEVEFEVEGNKVVDQTGVLSDSKKETTDDAFTTKIKDTSLIDLEMEDGLNGDVGTDANRKKNESNDAEVSENEDTTGLTSPTRVAKISSDQLENALEMGRQQDVTECIGNVLFQIESGSEPIRYDEDNEQYDLVKQLFYGTTKQSIVPLSATNKVRTKVERFLSLLINIGDHPKDIYDAFDSYFKDEYLTMEEYGDVIRTVAVTTFPTILQVQIQRVYYDRERLMPFKSIEPLPFKEVIYMDRYADTENPLLLAKKKETEEMKQKLKVMKNRQRELLSRDDSGLTRKDAFLESIKLLESDTIKKTPLKIEAANDVIKTLRNNVQNIDNELMKLYNDINSLEEKISHQFDDFKEYGYSLFSVFIHRGEASYGHYWIYIKDRNRNGIWRKYNDETISEVQEEEVFNFNEGNTATPYFLVYVKQGQEGDIEPLKRILK 6D106539AE5C5F3F cdc48-shp1-19 1 18 predetermined predetermined participant predetermined structure determination identification by structure determination identification by structure determination structure determination experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component physiological level physiological level endogenous level endogenous endogenous endogenous level FLAG Tag FLAG Tag 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 yeast Saccharomyces cerevisiae Baker's yeast 6 structure determination identification by structure determination identification by structure determination structure determination experimental particp experimental participant identification experimental particp unspecified role unspecified role neutral component neutral component physiological level physiological level endogenous level endogenous endogenous endogenous level yeast Saccharomyces cerevisiae Baker's yeast direct interaction direct interaction Fig 1, Table S1 shp1-cdc48-17 2 8 mudpit multidimensional protein identification technology mudpit experimental particp experimental participant identification experimental particp unspecified role unspecified role prey prey native native yeast Saccharomyces cerevisiae Baker's yeast 4 mudpit multidimensional protein identification technology mudpit experimental particp experimental participant identification experimental particp unspecified role unspecified role prey prey native native yeast Saccharomyces cerevisiae Baker's yeast 10 mudpit multidimensional protein identification technology mudpit experimental particp experimental participant identification experimental particp unspecified role unspecified role prey prey native native yeast Saccharomyces cerevisiae Baker's yeast 7 mudpit multidimensional protein identification technology mudpit experimental particp experimental participant identification experimental particp unspecified role unspecified role prey prey native native yeast Saccharomyces cerevisiae Baker's yeast 12 mudpit multidimensional protein identification technology mudpit experimental particp experimental participant identification experimental particp unspecified role unspecified role prey prey native native yeast Saccharomyces cerevisiae Baker's yeast 14 mudpit multidimensional protein identification technology mudpit experimental particp experimental participant identification experimental particp unspecified role unspecified role prey prey native native yeast Saccharomyces cerevisiae Baker's yeast 15 mudpit multidimensional protein identification technology mudpit experimental particp experimental participant identification experimental particp unspecified role unspecified role prey prey native native yeast Saccharomyces cerevisiae Baker's yeast 19 mudpit multidimensional protein identification technology mudpit experimental particp experimental participant identification experimental particp unspecified role unspecified role prey prey native native yeast Saccharomyces cerevisiae Baker's yeast 16 mudpit multidimensional protein identification technology mudpit experimental particp experimental participant identification experimental particp unspecified role unspecified role prey prey native native yeast Saccharomyces cerevisiae Baker's yeast 9 mudpit multidimensional protein identification technology mudpit experimental particp experimental participant identification experimental particp unspecified role unspecified role prey prey native native yeast Saccharomyces cerevisiae Baker's yeast 5 mudpit multidimensional protein identification technology mudpit experimental particp experimental participant identification experimental particp unspecified role unspecified role prey prey native native yeast Saccharomyces cerevisiae Baker's yeast 11 mudpit multidimensional protein identification technology mudpit experimental particp experimental participant identification experimental particp unspecified role unspecified role prey prey native native yeast Saccharomyces cerevisiae Baker's yeast 17 mudpit multidimensional protein identification technology mudpit experimental particp experimental participant identification experimental particp unspecified role unspecified role prey prey native native yeast Saccharomyces cerevisiae Baker's yeast 13 mudpit multidimensional protein identification technology mudpit experimental particp experimental participant identification experimental particp unspecified role unspecified role prey prey native native yeast Saccharomyces cerevisiae Baker's yeast 3 mudpit multidimensional protein identification technology mudpit experimental particp experimental participant identification experimental particp unspecified role unspecified role prey prey native native yeast Saccharomyces cerevisiae Baker's yeast 18 mudpit multidimensional protein identification technology mudpit experimental particp experimental participant identification experimental particp unspecified role unspecified role bait bait purified purified native native FLAG Tag FLAG Tag 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 yeast Saccharomyces cerevisiae Baker's yeast 6 mudpit multidimensional protein identification technology mudpit experimental particp experimental participant identification experimental particp unspecified role unspecified role prey prey purified purified native native yeast Saccharomyces cerevisiae Baker's yeast association association Fig S10