DIP Database of Interacting Proteins 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ dip@mbi.ucla.edu 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ han-2020-1 in vitro In vitro 3d-em-single electron microscopy 3D single particle reconstruction 3D-EM-single experimental particp experimental participant identification experimental particp Han Y., Reyes AA., Malik S., He Y. yuanhe@northwestern.edu Nature 2020 Only protein-protein interactions imex curation imex curation han-2020-2 yeast Saccharomyces cerevisiae Baker's yeast tap tandem affinity purification TAP TAP tap weight by comassie molecular weight estimation by coomasie staining weight by comassie Han Y., Reyes AA., Malik S., He Y. yuanhe@northwestern.edu Nature 2020 Only protein-protein interactions imex curation imex curation rt102_yeast Regulator of Ty1 transposition protein 102 RTT102 G9378 YGR275W protein protein yeast Saccharomyces cerevisiae Baker's yeast MDPQTLITKANKVSYYGNPTSKESWRYDWYQPSKVSSNVQQPQQQLGDMENNLEKYPFRYKTWLRNQEDEKNLQRESCEDILDLKEFDRRILKKSLMTSHTKGDTSKATGAPSANQGDEALSVDDIRGAVGNSEAIPGLSAGVNNDNTKESKDVKMN h2b11_xenla Histone H2B 1.1 protein protein xenla Xenopus laevis (African clawed frog) African clawed frog MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK h2a1_xenla Histone H2A type 1 protein protein xenla Xenopus laevis (African clawed frog) African clawed frog MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQSVLLPKKTESAKSAKSK h4_xenla Histone H4 protein protein xenla Xenopus laevis (African clawed frog) African clawed frog MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG h32_xenla Histone H3.2 protein protein xenla Xenopus laevis (African clawed frog) African clawed frog MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA arp9_yeast Actin-like protein ARP9 ARP9 SWP59 YMR033W YM9973.07 Chromatin structure-remodeling complex protein ARP9 SWI/SNF complex component ARP9 protein protein yeast Saccharomyces cerevisiae Baker's yeast MAPFRQDSILIIYPRSQTTLVQFGLNEETFTVPELEIPTQIYRTTRQDGSYTYHSTNKDNKAELIKPIQNGEIIDISAFTQFLRLIFVSILSDRANKNQDAFEAELSNIPLLLITHHSWSQSDLEIITQYVFESLEINNLIQLPASLAATYSMISLQNCCIIDVGTHHTDIIPIVDYAQLDHLVSSIPMGGQSINDSLKKLLPQWDDDQIESLKKSPIFEVLSDDAKKLSSFDFGNENEDEDEGTLNVAEIITSGRDTREVLEERERGQKVKNVKNSDLEFNTFWDEKGNEIKVGKQRFQGCNNLIKNISNRVGLTLDNIDDINKAKAVWENIIIVGGTTSISGFKEALLGQLLKDHLIIEPEEEKSKREEEAKSVLPAATKKKSKFMTNSTAFVPTIEYVQCPTVIKLAKYPDYFPEWKKSGYSEIIFLGAQIVSKQIFTHPKDTFYITREKYNMKGPAALWDVQF EE1AB154A906420E arp7_yeast Actin-related protein 7 ARP7 SWP61 YPR034W YP9367.14 Actin-like protein ARP7 Chromatin structure-remodeling complex protein ARP7 SWI/SNF complex component ARP7 protein protein yeast Saccharomyces cerevisiae Baker's yeast MTLNRKCVVIHNGSHRTVAGFSNVELPQCIIPSSYIKRTDEGGEAEFIFGTYNMIDAAAEKRNGDEVYTLVDSQGLPYNWDALEMQWRYLYDTQLKVSPEELPLVITMPATNGKPDMAILERYYELAFDKLNVPVFQIVIEPLAIALSMGKSSAFVIDIGASGCNVTPIIDGIVVKNAVVRSKFGGDFLDFQVHERLAPLIKEENDMENMADEQKRSTDVWYEASTWIQQFKSTMLQVSEKDLFELERYYKEQADIYAKQQEQLKQMDQQLQYTALTGSPNNPLVQKKNFLFKPLNKTLTLDLKECYQFAEYLFKPQLISDKFSPEDGLGPLMAKSVKKAGASINSMKANTSTNPNGLGTSHINTNVGDNNSTASSSNISPEQVYSLLLTNVIITGSTSLIEGMEQRIIKELSIRFPQYKLTTFANQVMMDRKIQGWLGALTMANLPSWSLGKWYSKEDYETLKRDRKQSQATNATN 8E105921576FA213 snf6_yeast Transcription regulatory protein SNF6 SNF6 YHL025W SWI/SNF complex component SNF6 protein protein yeast Saccharomyces cerevisiae Baker's yeast MGVIKKKRSHHGKASRQQYYSGVQVGGVGSMGAINNNIPSLTSFAEENNYQYGYSGSSAGMNGRSLTYAQQQLNKQRQDFERVRLRPEQLSNIIHDESDTISFRSNLLKNFISSNDAFNMLSLTTVPCDRIEKSRLFSEKTIRYLMQKQHEMKTQAAELQEKPLTPLKYTKLIAAAEDGSRSTKDMIDAVFEQDSHLRYQPDGVVVHRDDPALVGKLRGDLREAPADYWTHAYRDVLAQYHEAKERIRQKEVTAGEAQDEASLQQQQQQDLQQQQQVVTTVASQSPHATATEKEPVPAVVDDPLENMFGDYSNEPFNTNFDDEFGDLDAVFF ED9EA9F313F9079F snf12_yeast Transcription regulatory protein SNF12 SNF12 SWP73 YNR023W N3224 SWI/SNF complex component SWP73 protein protein yeast Saccharomyces cerevisiae Baker's yeast MSKVMKPSNGKGSRKSSKAATPDTKNFFHAKKKDPVNQDKANNASQITPTVPHSHPSDMVIPDHLAELIPELYSFQQLVDSEKRLDHFIHLRNLHMKRMVAQWERSKLSQEFLYPHLNFPNVKFLRIFISNVSENQPWQMDTNNEADLMALENATWTMRIEGRLLDNVQANDPAREKFSSFIESIVVDFKNKENDNVPSTKFNAAPEENATEGPSDKKLNLNLPLQFSLPNGDNSTTTNTDQNNATMGEETAKKDMSSTTPKLESVKWQYDPNNPVDFDGLDIKRVGSENVECTISILRKSSPEEPFMSYSPQLTAIIGLKSGTSHDAIFSIYKYIHLNELLTNDESAFENLMGNRNNHNSNTSTSKMLDAASSQVSIVKLDTQLITLLPSSLKESSPDTMKLTDLLSLINSTHLLPLQPIEIDYTVRVDKASTYGELVLDIEVPDVNALKFNNTQRESQIGAAELNENARELEQIKPKIALQDKEITSVLSNLHESNKRYRFFKKISEDPVKALNECIASTSNALKVLSGDEGYNEDMVRRANFYKENEAMLRENIEVILSNGRM CD6E61EEEE85098C swi3_yeast SWI/SNF complex subunit SWI3 SWI3 TYE2 J0495 YJL176C Transcription regulatory protein SWI3 Transcription factor TYE2 protein protein yeast Saccharomyces cerevisiae Baker's yeast MENTLGEGSTVNASVDVDQHGNDNNSDSNANAAVAGVANTDTAGEESQQQDESLKDEATVPNTRDAESEAITVTAKQQPTMQANKLDSQETPSTEESRAQNVFGQDNEDSDNLFGETESSVSNNEANTPSIPTNPVDNENNKPAIKEDSTIQDSNGDVKNMEDVKIQKEEEPENNTVIEGVKEESQPDENTKEMDEVEEDDEDDDQPMISPDNSIFGDTKSESKQLGNTSSVANTPSEIPDAHKAEQEDIIEKTESVDKKVDSGEERNEQEREIMNDHSKSANPKKTTITRVEPETFEIPQAHEIVIPSYSKWFNLEKIHSIEVQSLPEFFTNRIPSKTPEVYMRYRNFMVNSYRLNPNEYFSVTTARRNVSGDAAALFRLHKFLTKWGLINYQVDSKLLPKNIEPPLTSQYSTRHDAPRGLFPFESYKPSVQLPDMAKLKKMMNTSDSESTLYKYLKESKRKYDEITHPPSTTDDENGDKNDNGGKMNNEVSTSTSMTGDANLLEEGETSRPLKKVKILEQIDENWSKEDLQKLLKGIQEFGADWYKVAKNVGNKSPEQCILRFLQLPIEDKFLYGDGNGKGDNDNGLGPLKYAPHLPFSKSENPVLSTIAFLVGLVNPKTVQSMTQRAIQSAESIKSQKEEISDQKPIEHIKEGSEIAISSLGYRSHIFATNEERQMNFLTNELIRLQMEKLDAKLNHLKKLEKFMELERKTLERQQENLLIQRLNFNQNSSKIVNVLSKCLNLISDSNINNSSVAEKEEIRSQIDHFKSMLSKPETLSIGKNPFNKPNIETGENHNGQSISNENDVKPISIEAPQFYRYWSA DBA2E2022F15F9A6 snf5_yeast SWI/SNF chromatin-remodeling complex subunit SNF5 SNF5 SWI10 TYE4 YBR2036 YBR289W SWI/SNF complex subunit SNF5 Transcription regulatory protein SNF5 Transcription factor TYE4 protein protein yeast Saccharomyces cerevisiae Baker's yeast MNNQPQGTNSVPNSIGNIFSNIGTPSFNMAQIPQQLYQSLTPQQLQMIQQRHQQLLRSRLQQQQQQQQQTSPPPQTHQSPPPPPQQSQPIANQSATSTPPPPPAPHNLHPQIGQVPLAPAPINLPPQIAQLPLATQQQVLNKLRQQAIAKNNPQVVNAITVAQQQVQRQIEQQKGQQTAQTQLEQQRQLLVQQQQQQQLRNQIQRQQQQQFRHHVQIQQQQQKQQQQQQQHQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQGQIPQSQQVPQVRSMSGQPPTNVQPTIGQLPQLPKLNLPKYQTIQYDPPETKLPYPTYWSDKKADTDTLLYEQIIQRDKINKYSLIRETNGYDPFSIYGFSNKEYISRLWHTLKYYQDLKNTRMKSITSTSQKIPSASIWGNGYSGYGNGITNTTTRVIPQVEVGNRKHYLEDKLKVYKQAMNETSEQLVPIRLEFDQDRDRFFLRDTLLWNKNDKLIKIEDFVDDMLRDYRFEDATREQHIDTICQSIQEQIQEFQGNPYIELNQDRLGGDDLRIRIKLDIVVGQNQLIDQFEWDISNSDNCPEEFAESMCQELELPGEFVTAIAHSIREQVHMYHKSLALLGYNFDGSAIEDDDIRSRMLPTITLDDVYRPAAESKIFTPNLLQISAAELERLDKDKDRDTRRKRRQGRSNRRGMLALSGTSASNTSMNGVHNTVAAGNASSLPPGEILLPDIADIPRTFRTPVPSTLMPGGVDVGPSVESYELRNTTTYKSRPDRPKPVSPPCYIIDHIPGHSLLLSIKLPGKVNTKEEFAAAPNDTSSGTNAMLPSPESLKTKLNSNIRAGVTIPSIPNPIANHTVTNSPNPTLQPVIPGGAASKSVPTPSLPIAPPVAPHDSEATLLTNSNNGSSNNNTQNT F6D31A57E6D6DA94 swi1_yeast SWI/SNF chromatin-remodeling complex subunit SWI1 SWI1 ADR6 GAM3 Regulatory protein GAM3 SWI/SNF complex subunit SWI1 Transcription regulatory protein ADR6 Transcription regulatory protein SWI1 LPA1 YPL016W protein protein yeast Saccharomyces cerevisiae Baker's yeast MDFFNLNNNNNNNNTTTTTTTTNNNNTNNNNTNNNNNPANNTNNNNSTGHSSNTNNNTNNNNTNTGASGVDDFQNFFDPKPFDQNLDSNNNNSNSNNNDNNNSNTVASSTNFTSPTAVVNNAAPANVTGGKAANFIQNQSPQFNSPYDSNNSNTNLNSLSPQAILAKNSIIDSSNLPLQAQQQLYGGNNNNNSTGIANDNVITPHFITNVQSISQNSSSSTPNTNSNSTPNANQQFLPFNNSASNNGNLTSNQLISNYAASNSMDRSSSASNEFVPNTSDNNNNSNNHNMRNNSNNKTSNNNNVTAVPAATPANTNNSTSNANTVFSERAAMFAALQQKQQQRFQALQQQQQQQQNQQQQNQQPQQQQQQQQNPKFLQSQRQQQQRSILQSLNPALQEKISTELNNKQYELFMKSLIENCKKRNMPLQSIPEIGNRKINLFYLYMLVQKFGGADQVTRTQQWSMVAQRLQISDYQQLESIYFRILLPYERHMISQEGIKETQAKRIFLQQFLQELLKKVQQQQQAAALANANNNINSASSAPTPAAPGASVPATAAPGTEAGIVPVSANTPKSLNSNININVNNNNIGQQQVKKPRKQRVKKKTKKELELERKEREDFQKRQQKLLEDQQRQQKLLLETKLRQQYEIELKKLPKVYKRSIVRNYKPLINRLKHYNGYDINYISKIGEKIDSNKPIFLFAPELGAINLHALSMSLQSKNLGEINTALNTLLVTSADSNLKISLVKYPELLDSLAILGMNLLSNLSQNVVPYHRNTSDYYYEDAGSNQYYVTQHDKMVDKIFEKVNNNATLTPNDSNDEKVTILVDSLTGNQLPTPTPTEMEPDLDTECFISMQSTSPAVKQWDLLPEPIRFLPNQFPLKIHRTPYLTSLKKIKDEIDDPFTKINTRGAEDPKVLINDQLSTISMILRNISFSDNNSRIMSRNFYLKRFISDLLWLVLIHPENFTCNRKILNFKKDLVIVLSNISHLLEIASSIDCLLILILVISFGQPKLNPMASSSSFGSESLTFNEFQLQWGKYQTFGVDILAKLFSLEKPNLNYFKSILLNKNTGNNLYDRNSNNNHKDKKLLRRLLNLYNDNNKNNNNRHNLLNDVVSFLFSAIPLQQVLSQSADPSLLIDQFSPVISQSLTSILVIVQKILPLSNEVFEISENNSDSNSNNNGNKDSSFNFNKNLPFVWLSSEENIGSGLLKLSEIILNINNSTSKNTLLQQQNYSKVLLPSINISCVQLIKCLVEKSICFENCLNNDPEILKKIASIPNLFPTDLEIFQLFTNPSVDIQIINQYQLLYNLKNDILTNLE F442D5A82013CDBD snf2_yeast Transcription regulatory protein SNF2 SNF2 GAM1 SWI2 RIC1 TYE3 YOR290C ATP-dependent helicase SNF2 SWI/SNF complex component SNF2 Regulatory protein SWI2 Regulatory protein GAM1 Transcription factor TYE3 protein protein yeast Saccharomyces cerevisiae Baker's yeast MNIPQRQFSNEEVNRCYLRWQHLRNEHGMNAPSVPEFIYLTKVLQFAAKQRQELQMQRQQQGISGSQQNIVPNSSDQAELPNNASSHISASASPHLAPNMQLNGNETFSTSAHQSPIMQTQMPLNSNGGNNMLPQRQSSVGSLNATNFSPTPANNGENAAEKPDNSNHNNLNLNNSELQPQNRSLQEHNIQDSNVMPGSQINSPMPQQAQMQQAQFQAQQAQQAQQAQQAQQAQARLQQGRRLPMTMFTAEQSELLKAQITSLKCLVNRKPIPFEFQAVIQKSINHPPDFKRMLLSLSEFARRRQPTDQNNQSNLNGGNNTQQPGTNSHYNNTNTDNVSGLTRNAPLDSKDENFASVSPAGPSSVHNAKNGTLDKNSQTVSGTPITQTESKKEENETISNVAKTAPNSNKTHTEQNNPPKPQKPVPLNVLQDQYKEGIKVVDIDDPDMMVDSFTMPNISHSNIDYQTLLANSDHAKFTIEPGVLPVGIDTHTATDIYQTLIALNLDTTVNDCLDKLLNDECTESTRENALYDYYALQLLPLQKAVRGHVLQFEWHQNSLLTNTHPNFLSKIRNINVQDALLTNQLYKNHELLKLERKKTEAVARLKSMNKSAINQYNRRQDKKNKRLKFGHRLIATHTNLERDEQKRAEKKAKERLQALKANDEEAYIKLLDQTKDTRITHLLRQTNAFLDSLTRAVKDQQKYTKEMIDSHIKEASEEVDDLSMVPKMKDEEYDDDDDNSNVDYYNVAHRIKEDIKKQPSILVGGTLKDYQIKGLQWMVSLFNNHLNGILADEMGLGKTIQTISLLTYLYEMKNIRGPYLVIVPLSTLSNWSSEFAKWAPTLRTISFKGSPNERKAKQAKIRAGEFDVVLTTFEYIIKERALLSKVKWVHMIIDEGHRMKNAQSKLSLTLNTHYHADYRLILTGTPLQNNLPELWALLNFVLPKIFNSVKSFDEWFNTPFANTGGQDKIELSEEETLLVIRRLHKVLRPFLLRRLKKDVEKELPDKVEKVVKCKMSALQQIMYQQMLKYRRLFIGDQNNKKMVGLRGFNNQIMQLKKICNHPFVFEEVEDQINPTRETNDDIWRVAGKFELLDRILPKLKATGHRVLIFFQMTQIMDIMEDFLRYINIKYLRLDGHTKSDERSELLRLFNAPDSEYLCFILSTRAGGLGLNLQTADTVIIFDTDWNPHQDLQAQDRAHRIGQKNEVRILRLITTNSVEEVILERAYKKLDIDGKVIQAGKFDNKSTSEEQEALLRSLLDAEEERRKKRESGVEEEEELKDSEINEILARNDEEMAVLTRMDEDRSKKEEELGVKSRLLEKSELPDIYSRDIGAELKREESESAAVYNGRGARERKTATYNDNMSEEQWLRQFEVSDDEKNDKQARKQRTKKEDKSEAIDGNGEIKGENIDADNDGPRINNISAEDRADTDLAMNDDDFLSKKRKAGRPRGRPKKVKLEGSENSEPPALESSPVTGDNSPSEDFMDIPKPRTAGKTSVKSARTSTRGRGRGRGRGRGRGRGRGRPPKARNGLDYVRTPAAATSPIDIREKVAKQALDLYHFALNYENEAGRKLSDIFLSKPSKALYPDYYMIIKYPVAFDNINTHIETLAYNSLKETLQDFHLIFSNARIYNTEGSVVYEDSLELEKVVTKKYCEIMGDNSQLDFTEFDEQYGTRPLVLPPVVTSSVAESFTDEADSSMTEASV 84B8BC595C8F3E6D cryoem-1 3683011 N/A 3683013 structure determination identification by structure determination identification by structure determination structure determination unspecified role unspecified role neutral component neutral component purified purified yeast Saccharomyces cerevisiae Baker's yeast Stoichiometry: 1.0 N/A 3683014 structure determination identification by structure determination identification by structure determination structure determination unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 N/A 3683015 predetermined predetermined participant predetermined structure determination identification by structure determination identification by structure determination structure determination unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 N/A 3683016 structure determination identification by structure determination identification by structure determination structure determination unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 N/A 3683017 structure determination identification by structure determination identification by structure determination structure determination unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 N/A 3683018 structure determination identification by structure determination identification by structure determination structure determination unspecified role unspecified role neutral component neutral component purified purified yeast Saccharomyces cerevisiae Baker's yeast Stoichiometry: 1.0 N/A 3683019 structure determination identification by structure determination identification by structure determination structure determination unspecified role unspecified role neutral component neutral component purified purified yeast Saccharomyces cerevisiae Baker's yeast Stoichiometry: 1.0 N/A 3683020 structure determination identification by structure determination identification by structure determination structure determination unspecified role unspecified role neutral component neutral component purified purified yeast Saccharomyces cerevisiae Baker's yeast Stoichiometry: 1.0 N/A 3683021 structure determination identification by structure determination identification by structure determination structure determination unspecified role unspecified role neutral component neutral component purified purified yeast Saccharomyces cerevisiae Baker's yeast Stoichiometry: 1.0 N/A 3683022 structure determination identification by structure determination identification by structure determination structure determination unspecified role unspecified role neutral component neutral component purified purified yeast Saccharomyces cerevisiae Baker's yeast Stoichiometry: 4.0 N/A 3683023 structure determination identification by structure determination identification by structure determination structure determination unspecified role unspecified role neutral component neutral component purified purified yeast Saccharomyces cerevisiae Baker's yeast Stoichiometry: 1.0 N/A 3683024 structure determination identification by structure determination identification by structure determination structure determination unspecified role unspecified role neutral component neutral component purified purified yeast Saccharomyces cerevisiae Baker's yeast Stoichiometry: 1.0 N/A 3683025 structure determination identification by structure determination identification by structure determination structure determination unspecified role unspecified role neutral component neutral component purified purified yeast Saccharomyces cerevisiae Baker's yeast Stoichiometry: 1.0 physical association physical association false false false Supplementary Table 3 arp7-1 3683012 N/A 3683013 predetermined predetermined participant predetermined unspecified role unspecified role prey prey purified purified yeast Saccharomyces cerevisiae Baker's yeast N/A 3683018 predetermined predetermined participant predetermined unspecified role unspecified role prey prey purified purified yeast Saccharomyces cerevisiae Baker's yeast N/A 3683019 predetermined predetermined participant predetermined unspecified role unspecified role prey prey purified purified yeast Saccharomyces cerevisiae Baker's yeast N/A 3683020 predetermined predetermined participant predetermined unspecified role unspecified role prey prey purified purified yeast Saccharomyces cerevisiae Baker's yeast N/A 3683021 predetermined predetermined participant predetermined unspecified role unspecified role prey prey purified purified yeast Saccharomyces cerevisiae Baker's yeast N/A 3683022 predetermined predetermined participant predetermined unspecified role unspecified role prey prey purified purified yeast Saccharomyces cerevisiae Baker's yeast N/A 3683023 predetermined predetermined participant predetermined unspecified role unspecified role prey prey purified purified yeast Saccharomyces cerevisiae Baker's yeast N/A 3683024 predetermined predetermined participant predetermined unspecified role unspecified role prey prey purified purified yeast Saccharomyces cerevisiae Baker's yeast N/A 3683025 predetermined predetermined participant predetermined unspecified role unspecified role bait bait over-expressed over expressed level over-expressed purified purified TAP tag TAP tag tandem tag tandem tag 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 association association false false false ExtFig 1