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/ murthy-2014-1 A Crohn's disease variant in Atg16l1 enhances its degradation by caspase 3. in vitro In vitro protease assay protease assay anti tag western anti tag western blot anti tag western Murthy A., Li Y., Peng I., Reichelt M., Katakam A.K., Noubade R., Roose-Girma M., DeVoss J., Diehl L., Graham R.R., van Lookeren Campagne M. Crohn's disease - Interactions of proteins identified as having a link to Crohn's disease Processing of the thr300ala ATG16L1beta variant by caspase-1 and caspae-6 occured with lower efficiency compared to caspase-3. The expression system of recombinant human active caspases was obtained from the supplier's website (MBL International). menno@gene.com Nature (0028-0836) 2014 Only protein-protein interactions imex curation IBD - Inflammatory bowel disease murthy-2014-2 A Crohn's disease variant in Atg16l1 enhances its degradation by caspase 3. mouse-macrophage Mus musculus macrophage macrophage Macrophage fluorescence imaging fluorescence microscopy fluorescence imaging immunostaining immunostaining Murthy A., Li Y., Peng I., Reichelt M., Katakam A.K., Noubade R., Roose-Girma M., DeVoss J., Diehl L., Graham R.R., van Lookeren Campagne M. Crohn's disease - Interactions of proteins identified as having a link to Crohn's disease menno@gene.com Nature (0028-0836) 2014 Only protein-protein interactions imex curation IBD - Inflammatory bowel disease casp3_human Caspase-3 Apopain Cysteine protease CPP32 Protein Yama SREBP cleavage activity 1 CASP3 CPP32 protein protein human Homo sapiens Human MENTENSVDSKSIKNLEPKIIHGSESMDSGISLDNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKITNFFRGDRCRSLTGKPKLFIIQACRGTELDCGIETDSGVDDDMACHKIPVEADFLYAYSTAPGYYSWRNSKDGSWFIQSLCAMLKQYADKLEFMHILTRVNRKVATEFESFSFDATFHAKKQIPCIVSMLTKELYFYH a16l1_human Autophagy-related protein 16-1 APG16-like 1 UNQ9393/PRO34307 ATG16L1 APG16L protein protein human Homo sapiens Human MSSGLRAADFPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLLEKSDLHSVLAQKLQAEKHDVPNRHEISPGHDGTWNDNQLQEMAQLRIKHQEELTELHKKRGELAQLVIDLNNQMQRKDREMQMNEAKIAECLQTISDLETECLDLRTKLCDLERANQTLKDEYDALQITFTALEGKLRKTTEENQELVTRWMAEKAQEANRLNAENEKDSRRRQARLQKELAEAAKEPLPVEQDDDIEVIVDETSDHTEETSPVRAISRAATKRLSQPAGGLLDSITNIFGRRSVSSFPVPQDNVDTHPGSGKEVRVPATALCVFDAHDGEVNAVQFSPGSRLLATGGMDRRVKLWEVFGEKCEFKGSLSGSNAGITSIEFDSAGSYLLAASNDFASRIWTVDDYRLRHTLTGHSGKVLSAKFLLDNARIVSGSHDRTLKLWDLRSKVCIKTVFAGSSCNDIVCTEQCVMSGHFDKKIRFWDIRSESIVREMELLGKITALDLNPERTELLSCSRDDLLKVIDLRTNAIKQTFSAPGFKCGSDWTRVVFSPDGSYVAAGSAEGSLYIWSVLTGKVEKVLSKQHSSSINAVAWSPSGSHVVSVDKGCKAVLWAQY casp1_human Caspase-1 Interleukin-1 beta convertase Interleukin-1 beta-converting enzyme p45 CASP1 IL1BC IL1BCE protein protein human Homo sapiens Human MADKVLKEKRKLFIRSMGEGTINGLLDELLQTRVLNKEEMEKVKRENATVMDKTRALIDSVIPKGAQACQICITYICEEDSYLAGTLGLSADQTSGNYLNMQDSQGVLSSFPAPQAVQDNPAMPTSSGSEGNVKLCSLEEAQRIWKQKSAEIYPIMDKSSRTRLALIICNEEFDSIPRRTGAEVDITGMTMLLQNLGYSVDVKKNLTASDMTTELEAFAHRPEHKTSDSTFLVFMSHGIREGICGKKHSEQVPDILQLNAIFNMLNTKNCPSLKDKPKVIIIQACRGDSPGVVWFKDSVGVSGNLSLPTTEEFEDDAIKKAHIEKDFIAFCSSTPDNVSWRHPTMGSVFIGRLIEHMQEYACSCDVEEIFRKVRFSFEQPDGRAQMPTTERVTLTRCFYLFPGH casp6_human Caspase-6 Apoptotic protease Mch-2 CASP6 MCH2 protein protein human Homo sapiens Human MSSASGLRRGHPAGGEENMTETDAFYKREMFDPAEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTCADRDNLTRRFSDLGFEVKCFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEGNHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIFIIQACRGNQHDVPVIPLDVVDNQTEKLDTNITEVDAASVYTLPAGADFLMCYSVAEGYYSHRETVNGSWYIQDLCEMLGKYGSSLEFTELLTLVNRKVSQRRVDFCKDPSAIGKKQVPCFASMLTKKLHFFPKSN mlp3a_mouse Microtubule-associated proteins 1A/1B light chain 3A Map1lc3a Autophagy-related protein LC3 A Autophagy-related ubiquitin-like modifier LC3 A MAP1 light chain 3-like protein 1 MAP1A/MAP1B light chain 3 A Microtubule-associated protein 1 light chain 3 alpha protein protein mouse Mus musculus Mouse MPSDRPFKQRRSFADRCKEVQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMVSVSTPIADIYEQEKDEDGFLYMVYASQETFGF a16l1_mouse Autophagy-related protein 16-1 APG16-like 1 Atg16l1 Apg16l protein protein mouse Mus musculus Mouse MSSGLRAADFPRWKRHIAEELRRRDRLQRQAFEEIILQYTKLLEKSDLHSVLTQKLQAEKHDMPNRHEISPGHDGAWNDSQLQEMAQLRIKHQEELTELHKKRGELAQLVIDLNNQMQQKDKEIQMNEAKISEYLQTISDLETNCLDLRTKLQDLEVANQTLKDEYDALQITFTALEEKLRKTTEENQELVTRWMAEKAQEANRLNAENEKDSRRRQARLQKELAEAAKEPLPVEQDDDIEVIVDETSDHTEETSPVRAVSRAATKRLSQPAGGLLDSITNIFGRRSVSSIPVPQDIMDTHPASGKDVRVPTTASYVFDAHDGEVNAVQFSPGSRLLATGGMDRRVKLWEAFGDKCEFKGSLSGSNAGITSIEFDSAGAYLLAASNDFASRIWTVDDYRLRHTLTGHSGKVLSAKFLLDNARIVSGSHDRTLKLWDLRSKVCIKTVFAGSSCNDIVCTEQCVMSGHFDKKIRFWDIRSESVVREMELLGKITALDLNPERTELLSCSRDDLLKVIDLRTNAVKQTFSAPGFKCGSDWTRVVFSPDGSYVAAGSAEGSLYVWSVLTGKVEKVLSKQHSSSINAVAWAPSGLHVVSVDKGSRAVLWAQP atg16l1-casp3 1765311 n/a 1765313 enzyme enzyme neutral component neutral component ecolx Escherichia coli n/a 1765314 enzyme target enzyme target substrate substrate neutral component neutral component Q676U5:p.Thr300Ala mutation increasing rate mutation increasing interaction rate mutation increasing rate mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false c-terminus v5 tag v5 tag GKPIPNPLLGLDST epitope tag GKPIPNPLLGLDST epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false Q676U5:p.Asp299Glu mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false in vitro In vitro protein cleavage protein cleavage false false false Fig. 1b, Extended data fig. 1a P42574 is required for cleavage of Q676U5 P42574 increases degradation at protein level of Q676U5 atg16l1-casp1 1765311 n/a 1765314 enzyme target enzyme target substrate substrate neutral component neutral component Q676U5:p.Thr300Ala mutation increasing rate mutation increasing interaction rate mutation increasing rate mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false c-terminus v5 tag v5 tag GKPIPNPLLGLDST epitope tag GKPIPNPLLGLDST epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false in vitro In vitro n/a 1765315 enzyme enzyme neutral component neutral component ecolx Escherichia coli protein cleavage protein cleavage false false false Extended data fig. 1a P29466 is required for cleavage of Q676U5 atg16l1-casp6 1765311 n/a 1765316 enzyme enzyme neutral component neutral component ecolx Escherichia coli n/a 1765314 enzyme target enzyme target substrate substrate neutral component neutral component c-terminus v5 tag v5 tag GKPIPNPLLGLDST epitope tag GKPIPNPLLGLDST epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false Q676U5:p.Thr300Ala mutation increasing rate mutation increasing interaction rate mutation increasing rate mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false in vitro In vitro protein cleavage protein cleavage false false false Extended data fig. 1a P55212 is required for cleavage of Q676U5 atg16l1-map1lc3a 1765312 n/a 1765317 unspecified role unspecified role neutral component neutral component n/a 1765318 unspecified role unspecified role neutral component neutral component Q8C0J2:p.Thr300Ala mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false colocalization colocalization false false false Fig. 3a