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/ mcconnell-2004-1 Histone fold protein Dls1p is required for Isw2-dependent chromatin remodeling in vivo. yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast affinity chrom affinity chromatography technology Affinity purification Affinity purification affinity chrom ms participant Identification by mass spectrometry ms participant McConnell AD., Gelbart ME., Tsukiyama T. Chromatin - Epigenetic interactions resulting in chromatin modulation Complex purified by FLAG immunoaffinity chromatography followed by a Source Q anionic-exchange column. ttsukiya@fhcrc.org Mol. Cell. Biol. (0270-7306) 2004 Only protein-protein interactions imex curation mcconnell-2004-2 Histone fold protein Dls1p is required for Isw2-dependent chromatin remodeling in vivo. yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot McConnell AD., Gelbart ME., Tsukiyama T. Chromatin - Epigenetic interactions resulting in chromatin modulation Complex purified by FLAG immunoaffinity chromatography followed by a Source Q anionic-exchange column. ttsukiya@fhcrc.org Mol. Cell. Biol. (0270-7306) 2004 Only protein-protein interactions imex curation isw2_yeast ISWI chromatin-remodeling complex ATPase ISW2 ISW2 Imitation switch protein 2 YOR304W protein protein yeast Saccharomyces cerevisiae Baker's yeast MTTQQEEQRSDTKNSKSESPSEVLVDTLDSKSNGSSDDDNIGQSEELSDKEIYTVEDRPPEYWAQRKKKFVLDVDPKYAKQKDKSDTYKRFKYLLGVTDLFRHFIGIKAKHDKNIQKLLKQLDSDANKLSKSHSTVSSSSRHHRKTEKEEDAELMADEEEEIVDTYQEDIFVSESPSFVKSGKLRDYQVQGLNWLISLHENKLSGILADEMGLGKTLQTISFLGYLRYVKQIEGPFLIIVPKSTLDNWRREFLKWTPNVNVLVLHGDKDTRADIVRNIILEARFDVLITSYEMVIREKNALKRLAWQYIVIDEAHRIKNEQSALSQIIRLFYSKNRLLITGTPLQNNLHELWALLNFLLPDIFGDSELFDEWFEQNNSEQDQEIVIQQLHSVLNPFLLRRVKADVEKSLLPKIETNVYVGMTDMQIQWYKSLLEKDIDAVNGAVGKREGKTRLLNIVMQLRKCCNHPYLFEGAEPGPPYTTDEHLIFNSGKMIILDKLLKRLKEKGSRVLIFSQMSRLLDILEDYCYFRDFEYCRIDGSTSHEERIEAIDEYNKPNSEKFVFLLTTRAGGLGINLVTADTVILFDSDWNPQADLQAMDRAHRIGQKKQVHVYRFVTENAIEEKVIERAAQKLRLDQLVIQQGTGKKTASLGNSKDDLLDMIQFGAKNMFEKKASKVTVDADIDDILKKGEQKTQELNAKYQSLGLDDLQKFNGIENQSAYEWNGKSFQKKSNDKVVEWINPSRRERRREQTTYSVDDYYKEIIGGGSKSASKQTPQPKAPRAPKVIHGQDFQFFPKELDALQEKEQLYFKKKVNYKVTSYDITGDIRNEGSDAEEEEGEYKNAANTEGHKGHEELKRRIEEEQEKINSAPDFTQEDELRKQELISKAFTNWNKRDFMAFINACAKYGRDDMENIKKSIDSKTPEEVEVYAKIFWERLKEINGWEKYLHNVELGEKKNEKLKFQETLLRQKIEQCKHPLHELIIQYPPNNARRTYNTLEDKFLLLAVNKYGLRADKLYEKLKQEIMMSDLFTFDWFIKTRTVHELSKRVHTLLTLIVREYEQPDANKKKRSRTSATREDTPLSQNESTRASTVPNLPTTMVTNQKDTNDHVDKRTKIDQEA F71007D7B25C9348 dpb4_yeast DNA polymerase epsilon subunit D DPB4 DNA polymerase II subunit D YDR121W protein protein yeast Saccharomyces cerevisiae Baker's yeast MPPKGWRKDAQGNYPTTSYIKEQENITIQDLLFPKSTIVNLAREVPQQSGKKLLINKDASLALQRGATVFVNHLLLFAREIAKSQDKKSCSVDDVLSALDHIGHSALKGPVRDKLDEYQAAVEQRKKEKLDSGEVDADGDIDMGEDKENVPVEKVKEHDEIEEQGDALQDVEESSEKKQKTESQDVETRVQNLEQT dls1_yeast Protein DLS1 YJL065C J1115 HRD167 DPB3-like subunit of ISW2 complex 1 DLS1 protein protein yeast Saccharomyces cerevisiae Baker's yeast MNNETSGKETASAPLCSPKLPVEKVQRIAKNDPEYMDTSDDAFVATAFATEFFVQVLTHESLHRQQQQQQQQVPPLPDELTLSYDDISAAIVHSSDGHLQFLNDVIPTTKNLRLLVEENRVRYTTSVMPPNEVYSAYVVNDTAPKPNIVEIDLDNDEDDDEDVTDQE itc1_yeast Imitation switch two complex protein 1 G2842 YGL133W ITC1 protein protein yeast Saccharomyces cerevisiae Baker's yeast MVLYKRKPILLPDPKPLPLDLNVQVWHIEETGEWFSSYEEFLERFDFYTRHHFTCEITGTSCLTFFQALDSEETQFKYVEDRFPLKLREPVARFLHFNGIRRLDALVEKVYARFKNDFFPGEVVYLRKQKDSSTTSSNSQQSTPQPDDMVEINSVGNPGLPQYQYQRRYVIKEKVQFNATINPESREIVMPAHTKYMLIEEAASSNKSFIVDQGQIYRDRSTFTKHLIKCFFKITLQRASSKMGAPWCVKPEYLAMYGLTMEWPKDMLKYKEDEPVVARRSNSANVSSPESEKNKRQSKSSGKSNTSNDASNKKETKKKRKPTEVNDSENNSSEEDKKKGQNVTSETHSKKRKKEANEEPNTENVESVPTPANAEPQAVTITSIMDDLALPYQHPPNIFPNLTYYNEKLECISLGSTKLSRPFDSFGKLLQAYQFLNTFGSKICLSHFSLDQFITSLKCTDPYELKGEVVLVNIRTQTSKEQEIENNGLPMKNKAETTTEEDSENPSDWQRNSFIRDMIMKRNSDKVEYKIVHDDPASDDILDNINHNGSALLIEVFTALLRLFINEEGDWSCIVVENWIIDDKGVLMERKDERGEGEAKQKRNAHGYFLQDKEKIDNLKDTLKENATEVQKESDAKNETNSESDSKSDSDSEERDPKLEKCLNYRNVNWIERLTKRQFNNSYWLIILLGVLEDCRHLPMYTEFIDSFIEKIIPKDISATQLPKQLWRNFCRKLSFSDKVNALWILVDLVSHFSPDIKAAVDDSMELCGQIRSERFKVARELKTEAAVLSNLQGDLQAIQEKLNKTDENTPSADGADKKDDSESNSEPIDLIIIEKKQKLIEEQDKKVQALQSDKNFLDNCLFENDLQRLKPLGLDRYGNRYFWLDHNGVPFPQYPAGMNETPKSNNSLSYHSGRLLIQGPKASSAKFFLNVSDEQLSNWQKIRNSEGISEATREVFGISKTSSGSYNYVENGIEVELLDSNDRVNPLIELTPIQKKIMDETPSRLLLSPDQWYCIDKLEDLSRIMDWLDNWGRKEHDLLRQIRPIMERIKSSLSLRDHALSLTAFTKNEEKLLKELENNEFTENELNVDSMDVDDKNSGVKSEVDVQVDAEEKREAVIDEKLEVIADELMKLDDSSKTRNVLNRIQELEDQRDELLEQKKSIINSQRPGARILARSERKRTKISRGNKVNKQIEILTDLVNYRHFKAMEDVIAWKNVLANSIWGSSLRKNASGNKRSGVIETVDDKLKDIVGQTSRTVTPAPN dpoe_yeast DNA polymerase epsilon catalytic subunit A POL2 DUN2 YNL262W N0825 DNA polymerase II subunit A 3'-5' exodeoxyribonuclease protein protein yeast Saccharomyces cerevisiae Baker's yeast MMFGKKKNNGGSSTARYSAGNKYNTLSNNYALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVGWLTNMHATLVSQETLSSGSNGGGNSNDGERVTTNQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDESRVNDVEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSNQLFEARKLLRPILQDNANNNVQRNIYNVAANGSEKVDAKHLIEDIREYDVPYHVRVSIDKDIRVGKWYKVTQQGFIEDTRKIAFADPVVMAFDIETTKPPLKFPDSAVDQIMMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNENDEVALLQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGFAPDAEGEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIELDPELMTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNPDETLRKGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETYVGGHVESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSSVDKVTNFEEIKNQITQKLLELKENNIRNELPLIYHVDVASMYPNIMTTNRLQPDSIKAERDCASCDFNRPGKTCARKLKWAWRGEFFPSKMDEYNMIKRALQNETFPNKNKFSKKKVLTFDELSYADQVIHIKKRLTEYSRKVYHRVKVSEIVEREAIVCQRENPFYVDTVKSFRDRRYEFKGLAKTWKGNLSKIDPSDKHARDEAKKMIVLYDSLQLAHKVILNSFYGYVMRKGSRWYSMEMAGITCLTGATIIQMARALVERVGRPLELDTDGIWCILPKSFPETYFFTLENGKKLYLSYPCSMLNYRVHQKFTNHQYQELKDPLNYIYETHSENTIFFEVDGPYKAMILPSSKEEGKGIKKRYAVFNEDGSLAELKGFELKRRGELQLIKNFQSDIFKVFLEGDTLEGCYSAVASVCNRWLDVLDSHGLMLEDEDLVSLICENRSMSKTLKEYEGQKSTSITTARRLGDFLGEDMVKDKGLQCKYIISSKPFNAPVTERAIPVAIFSADIPIKRSFLRRWTLDPSLEDLDIRTIIDWGYYRERLGSAIQKIITIPAALQGVSNPVPRVEHPDWLKRKIATKEDKFKQTSLTKFFSKTKNVPTMGKIKDIEDLFEPTVEEDNAKIKIARTTKKKAVSKRKRNQLTNEEDPLVLPSEIPSMDEDYVGWLNYQKIKWKIQARDRKRRDQLFGNTNSSRERSALGSMIRKQAESYANSTWEVLQYKDSGEPGVLEVFVTINGKVQNITFHIPKTIYMKFKSQTMPLQKIKNCLIEKSSASLPNNPKTSNPAGGQLFKITLPESVFLEEKENCTSIFNDENVLGVFEGTITPHQRAIMDLGASVTFRSKAMGALGKGIQQGFEMKDLSMAENERYLSGFSMDIGYLLHFPTSIGYEFFSLFKSWGDTITILVLKPSNQAQEINASSLGQIYKQMFEKKKGKIETYSYLVDIKEDINFEFVYFTDISKLYRRLSQETTKLKEERGLQFLLLLQSPFITKLLGTIRLLNQMPIVKLSLNEVLLPQLNWQPTLLKKLVNHVLSSGSWISHLIKLSQYSNIPICNLRLDSMDYIIDVLYARKLKKENIVLWWNEKAPLPDHGGIQNDFDLNTSWIMNDSEFPKINNSGVYDNVVLDVGVDNLTVNTILTSALINDAEGSDLVNNNMGIDDKDAVINSPSEFVHDAFSNDALNVLRGMLKEWWDEALKENSTADLLVNSLASWVQNPNAKLFDGLLRYHVHNLTKKALLQLVNEFSALGSTIVYADRNQILIKTNKYSPENCYAYSQYMMKAVRTNPMFSYLDLNIKRYWDLLIWMDKFNFSGLACIEIEEKENQDYTAVSQWQLKKFLSPIYQPEFEDWMMIILDSMLKTKQSYLKLNSGTQRPTQIVNVKKQDKEDSVENSLNGFSHLFSKPLMKRVKKLFKNQQEFILDPQYEADYVIPVLPGSHLNVKNPLLELVKSLCHVMLLSKSTILEIRTLRKELLKIFELREFAKVAEFKDPSLSLVVPDFLCEYCFFISDIDFCKAAPESIFSCVRCHKAFNQVLLQEHLIQKLRSDIESYLIQDLRCSRCHKVKRDYMSAHCPCAGAWEGTLPRESIVQKLNVFKQVAKYYGFDILLSCIADLTI CBCDDE2AB147D65B isw2-dls1-1 Interaction between ASW2, DLP1 and DBP4 determined by affinity chromatography 608198 N/A 608200 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 608201 unspecified role unspecified role prey prey N/A 608202 unspecified role unspecified role prey prey association association false false false 1A isw2-dls1-2 Interaction between ASW2, DLP1, ITC1 and DBP4 determined by affinity chromatography 608198 N/A 608203 unspecified role unspecified role prey prey N/A 608202 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 608200 unspecified role unspecified role prey prey N/A 608201 unspecified role unspecified role prey prey association association false false false 1B dpb4-isw2-1 Interaction of Dpb4 with Isw2 and Pol2 identified by coimmunoprecipitation 608199 N/A 608200 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 608204 unspecified role unspecified role prey prey 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 608201 unspecified role unspecified role bait bait region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false association association false false false Immunodepletion studies suggested both prey proteins bound to DPB4 Fig. 2A dsl1-isw2-1 Interaction of Dsl1 with Isw2 and itc1 identified by coimmunoprecipitation 608199 N/A 608203 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 608202 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 608200 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 association association false false false Immunodepletion of Dls1 resulted in a partial depletion of both Isw2 and Itc1, suggesting the presence of Isw2 and Itc1 populations that do not stably interact with Dls1. Fig. 2C