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/ rao-2013-4 yeast Saccharomyces cerevisiae Baker's yeast anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Rao L., Romes EM., Nicholas MP., Brenner S., Tripathy A., Gennerich A., Slep KC. arne.gennerich@einstein.yu.edu, kslep@bio.unc.edu Molecular biology of the cell 2013 Only protein-protein interactions imex curation imex curation rao-2013-1 in vitro In vitro itc isothermal titration calorimetry ITC ITC itc predetermined predetermined participant predetermined Rao L., Romes EM., Nicholas MP., Brenner S., Tripathy A., Gennerich A., Slep KC. arne.gennerich@einstein.yu.edu, kslep@bio.unc.edu Molecular biology of the cell 2013 Only protein-protein interactions imex curation imex curation rao-2013-2 in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Rao L., Romes EM., Nicholas MP., Brenner S., Tripathy A., Gennerich A., Slep KC. arne.gennerich@einstein.yu.edu, kslep@bio.unc.edu Molecular biology of the cell 2013 Only protein-protein interactions imex curation imex curation rao-2013-3 in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Rao L., Romes EM., Nicholas MP., Brenner S., Tripathy A., Gennerich A., Slep KC. arne.gennerich@einstein.yu.edu, kslep@bio.unc.edu Molecular biology of the cell 2013 Only protein-protein interactions imex curation imex curation rao-2013-5 yeast Saccharomyces cerevisiae Baker's yeast fluorescence imaging fluorescence microscopy fluorescence imaging immunocytochemistry immunocytochemistry Rao L., Romes EM., Nicholas MP., Brenner S., Tripathy A., Gennerich A., Slep KC. arne.gennerich@einstein.yu.edu, kslep@bio.unc.edu Molecular biology of the cell 2013 Only protein-protein interactions imex curation imex curation pac11_yeast WD repeat-containing protein PAC11 PAC11 YDR488C protein protein yeast Saccharomyces cerevisiae Baker's yeast MERLKQLEEKRRQLKELRERRKQASLFPGSETMGHHPTEVHAKATMVSVSVQTDMEEGSKIQEPQSAYLRRKEVITYDKGIQTDQIEEEQLQENENHTTTDAVAIETTAADENNKDKAENDQPRLELAKPFLVEEAAATLSNASFARLETEVSASGQQAPSNMQQDKDNLMQWNMVSENLQSETDCDCIAQEYDPGKGVLVVVYLRLPPADLQYASSEAAWSVVNVVKCDNASGRNGLLIDMVEFRGTRIMTATILRRYHPESNVISILLATLTGKIILYELRLKQKKPETPVVYVVQRNMVARHYFQHPVVAVIETSSVQDQERVLVAADNGNIMELSCLDLTVLRKPQQLRPVPLSQLLSLENDTCTYTERLQRLAKFDEVGIACMAYTSEDPQYVWIGGEDGGIYKVFWDQPGPLYLSLDNNGFQPAENHSTRVTGLEFHWDDARRLMLLLSCSTDWTVRLWDARAGKAIIGAPLLLGGPVLRARWLEKNNGGENSRTLRCQVWCADGRLVVVNWAFDAKTSLYTATVIS 2037021799414E9A dyl1_yeast Dynein light chain 1, cytoplasmic DYN2 SLC1 YDR424C protein protein yeast Saccharomyces cerevisiae Baker's yeast MSDENKSTPIVKASDITDKLKEDILTISKDALDKYQLERDIAGTVKKQLDVKYGNTWHVIVGKNFGSYVTHEKGHFVYFYIGPLAFLVFKTA C25A690F35C3CEEC dyhc_yeast Dynein heavy chain, cytoplasmic DYN1 DHC1 Dynein heavy chain, cytosolic YKR054C protein protein yeast Saccharomyces cerevisiae Baker's yeast MCKNEARLANELIEFVAATVTGIKNSPKENEQAFIDYLHCQYLERFQFFLGLLDGREFDTLFVFLFEELDRTIVTIDIGEEAIYDANLANKKYSTLLIIKSRSVIVDAEPIATQISAIYLPGPVNAGNLASIITHGVSSVFGQLIKSDTKTYSVETIDKTRRKLDDISKQFQQLHTSIETPDLLAMVPSIIKLAVSKGATSHDYANYLPSNDLESMRFLNILQSIANKWFLVLKQTLAIDRDIKNGSFLDEVEFWSNFYEVLKSLIEQTQSQEFQVCLSVLTNAKRFHNLTNLLNEGSLSDKFKLADKYNQFLSSIPIDEVRQASNLEDLQELFPVLASSLKKFRYSGYPVQRFVVLMDKISQEVMDAILSNLSDLFQLEYGSFLGLYEKSAGMIEEWDDIVQDVNLLIREDLRKRAPQELLIQKLTFTSASVKATLDEILSTRKRFFSLAETIKSISPSTYHEEIQRLYHPFEQIHDISVNFRLKLEQAESEFSKNMLDLEKKLQNTLASFMDSDHCPTEKLSYLVKFKPLMELCPRIKVKVLENQQILLLEIKKDIRQLETGLELLPKILHVEALNNIPPISARISYFLNVQSRIDNIVQYLEALFGSNWNDTLEGRSISTSIVQLRKETNPHDVFLHWLGNFPEKATANLLTTPILKLIRNNEDDYELKVNFDFALAAAYSELRSLTYMAFQVPSHIVRIARTYMYLYPRAINLVELIQTFFSLSKSLSYTFYTNIFLKRNVQTVWLLLQQILITPWESLQEESSEMSCSVHSLARLEKSIDGILSDYQILKNSEPQFAKEFSGLKSFDGTADDLHEVEEIISNIQAIFENLFTKGLTNVSDHISTFNNLIISIILEKVRLNLKKMHFPKHVLKLSFNEGRITSSPSLAAMKRSLLKDIEALLNKVVLINFLHDPDHPLSTTLTFNSLVIKLKDDIQNCIEQVQNLHCKINSYVKEWQKMEFLWQITEEAFLEVVDNSTQRCFGILKGLLDSQSKFDLIISRNNFSKNLVLHTEDAQRHIRSKMDSWILYVSKHLLTIYERDARKLHEDMNRDREAVEDMDINFTSLKNITVIIEAVNVNKRHLTERDIQIKLLGSVMRALTKLKVRFPSHFVYIDQLDNDFSSLRQSLSYVEQELQKHRVVIAKSLEEGVENINNLSQSLNESWSVRKPISPTLTPPEALKILEFFNESITKLKKKMHSVAAAAKMLLIPVVLNDQLTHVVEEVKTYDLVWRSIKNLWEDVQRTFETPWCRVDVLLLQSDLANFLRRADELPRAVKQFEMYKSLFSQVNMLTSVNKILVELKDGALKPRHWNMIFRDIGKRQIQKNLLDKLEFSLKDVMVLNLTLNEILLTKIIERAQKEFVIEKSLNRIKKFWKEAQYEVIEHSSGLKLVREWDVLEQACKEDLEELVSMKASNYYKIFEQDCLDLESKLTKLSEIQVNWVEVQFYWLDLYGILGENLDIQNFLPLETSKFKSLTSEYKMITTRAFQLDTTIEVIHIPNFDTTLKLTIDSLKMIKSSLSTFLERQRRQFPRFYFLGNDDLLKIIGSGKHHDQVSKFMKKMFGSIESIIFLEDFITGVRSVEGEVLNLNEKIELKDSIQAQEWLNILDTEIKLSVFTQFRDCLGQLKDGTDIEVVVSKYIFQAILLSAQVMWTELVEKCLQTNQFSKYWKEVDMKIKGLLDKLNKSSDNVKKKIEALLVEYLHFNNVIGQLKNCSTKEEARLLWAKVQKFYQKNDTLDDLNSVFISQSGYLLQYKFEYIGIPERLIYTPLLLIGFATLTDSLHQKYGGCFFGPAGTGKTETVKAFGQNLGRVVVVFNCDDSFDYQVLSRLLVGITQIGAWGCFDEFNRLDEKVLSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPGYNGRSELPENLKKSFREFSMKSPQSGTIAEMILQIMGFEDSKSLASKIVHFLELLSSKCSSMNHYHFGLRTLKGVLRNCSPLISEFGEGEKTVVESLKRVILPSLGDTDELVFKDELSKIFDSAGTPLNSKAIVQCLKDAGQRSGFSMSEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATWKTVIDAMAIFDGHANVVYVIDTKVLTKESLYGSMLKATLEWRDGLFTSILRRVNDDITGTFKNSRIWVVFDSDLDPEYVEAMNSVLDDNKILTLPNGERLPIPPNFRILFETDNLDHTTPATITRCGLLWFSTDVCSISSKIDHLLNKSYEALDNKLSMFELDKLKDLISDSFDMASLTNIFTCSNDLVHILGVRTFNKLETAVQLAVHLISSYRQWFQNLDDKSLKDVITLLIKRSLLYALAGDSTGESQRAFIQTINTYFGHDSQELSDYSTIVIANDKLSFSSFCSEIPSVSLEAHEVMRPDIVIPTIDTIKHEKIFYDLLNSKRGIILCGPPGSGKTMIMNNALRNSSLYDVVGINFSKDTTTEHILSALHRHTNYVTTSKGLTLLPKSDIKNLVLFCDEINLPKLDKYGSQNVVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFTRHAAILYLGYPSGKSLSQIYEIYYKAIFKLVPEFRSYTEPFARASVHLYNECKARYSTGLQSHYLFSPRELTRLVRGVYTAINTGPRQTLRSLIRLWAYEAWRIFADRLVGVKEKNSFEQLLYETVDKYLPNQDLGNISSTSLLFSGLLSLDFKEVNKTDLVNFIEERFKTFCDEELEVPMVIHESMVDHILRIDRALKQVQGHMMLIGASRTGKTILTRFVAWLNGLKIVQPKIHRHSNLSDFDMILKKAISDCSLKESRTCLIIDESNILETAFLERMNTLLANADIPDLFQGEEYDKLLNNLRNKTRSLGLLLDTEQELYDWFVGEIAKNLHVVFTICDPTNNKSSAMISSPALFNRCIINWMGDWDTKTMSQVANNMVDVIPMEFTDFIVPEVNKELVFTEPIQTIRDAVVNILIHFDRNFYQKMKVGVNPRSPGYFIDGLRALVKLVTAKYQDLQENQRFVNVGLEKLNESVLKVNELNKTLSKKSTELTEKEKEARSTLDKMLMEQNESERKQEATEEIKKILKVQEEDIRKRKEVVMKSIQDIEPTILEAQRGVKNIKKQQLTEIRSMVNPPSGVKIVMEAVCAILGYQFSNWRDIQQFIRKDDFIHNIVHYDTTLHMKPQIRKYMEEEFLSDPNFTYETINRASKACGPLYQWVNAQINFSKVLENVDPLRQEMKRIEFESLKTKANLLAAEEMTQDLEASIEVSKRKYSLLIRDVEAIKTEMSNVQANLDRSISLVKSLTFEKERWLNTTKQFSKTSQELIGNCIISSIYETYFGHLNERERADMLVILKRLLGKFAVKYDVNYRFIDYLVTLDEKMKWLECGLDKNDYFLENMSIVMNSQDAVPFLLDPSSHMITVISNYYGNKTVLLSFLEEGFVKRLENAIRFGSVVIIQDGEFFDPIISRLISREFNHAGNRVTVEIGDHEVDVSGDFKLFIHSCDPSGDIPIFLRSRVRLVHFVTNKESIETRIFDITLTEENAEMQRKREDLIKLNTEYKLKLKNLEKRLLEELNNSQGNMLENDELMVTLNNLKKEAMNIEKKLSESEEFFPQFDNLVEEYSIIGKHSVKIFSMLEKFGQFHWFYGISIGQFLSCFKRVFIKKSRETRAARTRVDEILWLLYQEVYCQFSTALDKKFKMIMAMTMFCLYKFDIESEQYKEAVLTMIGVLSESSDGVPKLTVDTNNDLRYLWDYVTTKSYISALNWFKNEFFVDEWNIADVVANSENNYFTMASERDVDGTFKLIELAKASKESLKIIPLGSIENLNYAQEEISKSKIEGGWILLQNIQMSLSWVKTYLHKHVEETKAAEEHEKFKMFMTCHLTGDKLPAPLLQRTDRFVYEDIPGILDTVKDLWGSQFFTGKISGVWSVYCTFLLSWFHALITARTRLVPHGFSKKYYFNDCDFQFASVYLENVLATNSTNNIPWAQVRDHIATIVYGGKIDEEKDLEVVAKLCAHVFCGSDNLQIVPGVRIPQPLLQQSEEEERARLTAILSNTIEPADSLSSWLQLPRESILNYERLQAKEVASSTEQLLQEM dyn1-dyn2-1 3134420 N/A 3134425 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 3134426 unspecified role unspecified role prey prey N/A 3134427 unspecified role unspecified role bait bait n-terminal zz tag zz tag ZZ tag ZZ tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false n-terminal gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false n-terminal ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false c-terminal halotag tag tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false association association false false false Fig. 7A dyn1-pac11-1 3134420 N/A 3134425 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 3134427 unspecified role unspecified role bait bait n-terminal zz tag zz tag ZZ tag ZZ tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false n-terminal gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false n-terminal ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false c-terminal halotag tag tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false physical association physical association false false false Fig. 7A Interaction observed in DYN2-/- cells dyn2-pac11-2 3134421 N/A 3134426 unspecified role unspecified role neutral component neutral component Q02647:p.[Phe76Lys;Tyr78Glu] mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false Q02647:p.His58Lys mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 N/A 3134425 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 2.0 direct interaction direct interaction false false false 3134421 Fig. 1C, 5C, 5E, Supp fig 3 dyn2-pac11-3 3134422 N/A 3134426 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 N/A 3134425 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 2.0 direct interaction direct interaction false false false Table 1 1.9A Rworking 0.16 Rfree 0.212 dyn2-1 3134423 N/A 3134426 unspecified role unspecified role neutral component neutral component Q02647:p.[Phe76Lys;Tyr78Glu] mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false Q02647:p.His58Lys mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false yeast Saccharomyces cerevisiae Baker's yeast Stoichiometry: 2.0 direct interaction direct interaction false false false Fig. 5B, supp fig S2 dyn1-pac11-2 3134424 N/A 3134425 unspecified role unspecified role neutral component neutral component region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 3134427 tag fluorescence tag visualisation by fluorescence tag fluorescence unspecified role unspecified role neutral component neutral component n-terminal gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false n-terminal ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false c-terminal halotag tag tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false c-terminal tetramethyl rhodamine label tetramethyl rhodamine label c-term range C-terminal range c-term range c-term range C-terminal range c-term range false N/A 3134426 unspecified role unspecified role ancillary ancillary colocalization colocalization false false false Fig. 7B, Supp fig 4 TMR labelling of HALO tag. Colocalization is not observed in the absence of DYN2