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/ hakonen-2017-1 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid predetermined predetermined participant predetermined Hakonen JE., Sorrentino V., Avagliano Trezza R., de Wissel MB., van den Berg M., Bleijlevens B., van Ruissen F., Distel B., Baas F., Zelcer N., Weterman MAJ. Rare diseases - Interactions investigated in the context of Rare genetic disease LRSAM1 was found to be of human origin (pmid: 2012984) | Figure 5 ubiquitin ligase assay was not captured as name of ubiquitin enzyme (UbcH5a) was not informative enough to select the Uniprot ID; and usage of Ubc13 or Uev1a enzyme does not allow us to interpret the correct enzyme n.zelcer@amc.uva.nl,m.a.j.weterman@lumc.nl,m.a.weterman@amc.uva.nl Human molecular genetics 2017 Only protein-protein interactions imex curation imex curation hakonen-2017-2 human-293t Homo sapiens 293 cells transformed with SV40 large T antigen 293t 293 cells expressing SV40 large T antigen. The original designation of this cell line was 293tsA1609neo. It is not in Cabri,ATCC or HyperCLDB. anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Hakonen JE., Sorrentino V., Avagliano Trezza R., de Wissel MB., van den Berg M., Bleijlevens B., van Ruissen F., Distel B., Baas F., Zelcer N., Weterman MAJ. Rare diseases - Interactions investigated in the context of Rare genetic disease LRSAM1 was found to be of human origin (pmid: 2012984) and TSG101 construct was found to be of mouse origin (pmids: 14761944 & 11943869) n.zelcer@amc.uva.nl,m.a.j.weterman@lumc.nl,m.a.weterman@amc.uva.nl Human molecular genetics 2017 Only protein-protein interactions imex curation imex curation lrsm1_human E3 ubiquitin-protein ligase LRSAM1 Leucine-rich repeat and sterile alpha motif-containing protein 1 Tsg101-associated ligase LRSAM1 TAL UNQ6496/PRO21356 RING-type E3 ubiquitin transferase LRSAM1 protein protein human Homo sapiens Human MPLFFRKRKPSEEARKRLEYQMCLAKEAGADDILDISKCELSEIPFGAFATCKVLQKKVLIVHTNHLTSLLPKSCSLLSLATIKVLDLHDNQLTALPDDLGQLTALQVLNVERNQLMQLPRSIGNLTQLQTLNVKDNKLKELPDTVGELRSLRTLNISGNEIQRLPQMLAHVRTLEMLSLDASAMVYPPREVCGAGTAAILQFLCKESGLEYYPPSQYLLPILEQDGIENSRDSPDGPTDRFSREELEWQNRFSDYEKRKEQKMLEKLEFERRLELGQREHTQLLQQSSSQKDEILQTVKEEQSRLEQGLSEHQRHLNAERQRLQEQLKQTEQNISSRIQKLLQDNQRQKKSSEILKSLENERIRMEQLMSITQEETESLRRRDVASAMQQMLTESCKNRLIQMAYESQRQNLVQQACSSMAEMDERFQQILSWQQMDQNKAISQILQESAMQKAAFEALQVKKDLMHRQIRSQIKLIETELLQLTQLELKRKSLDTESLQEMISEQRWALSSLLQQLLKEKQQREEELREILTELEAKSETRQENYWLIQYQRLLNQKPLSLKLQEEGMERQLVALLEELSAEHYLPIFAHHRLSLDLLSQMSPGDLAKVGVSEAGLQHEILRRVQELLDAARIQPELKPPMGEVVTPTAPQEPPESVRPSAPPAELEVQASECVVCLEREAQMIFLNCGHVCCCQQCCQPLRTCPLCRQDIAQRLRIYHSS ube2b_rabit Ubiquitin-conjugating enzyme E2 B RAD6 homolog B RAD6B Ubiquitin carrier protein B Ubiquitin-conjugating enzyme E2(14k) Ubiquitin-protein ligase B UBE2B E2 ubiquitin-conjugating enzyme B protein protein rabit Oryctolagus cuniculus (Rabbit) Rabbit MSTPARRRLMRDFKRLQEDPPVGVSGAPSENNIMQWNAVIFGPEGTPFEDGTFKLVIEFSEEYPNKPPTVRFLSKMFHPNVYADGSICLDILQNRWSPTYDVSSILTSIQSLLDEPNPNSPANSQAAQLYQENKREYEKRVSAIVEQSWNDS ts101_mouse Tumor susceptibility gene 101 protein Tsg101 ESCRT-I complex subunit TSG101 protein protein mouse Mus musculus Mouse MAVSESQLKKMMSKYKYRDLTVRQTVNVIAMYKDLKPVLDSYVFNDGSSRELVNLTGTIPVRYRGNIYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTGKHVDANGKIYLPYLHDWKHPRSELLELIQIMIVIFGEEPPVFSRPTVSASYPPYTATGPPNTSYMPGMPSGISAYPSGYPPNPSGYPGCPYPPAGPYPATTSSQYPSQPPVTTVGPSRDGTISEDTIRASLISAVSDKLRWRMKEEMDGAQAELNALKRTEEDLKKGHQKLEEMVTRLDQEVAEVDKNIELLKKKDEELSSALEKMENQSENNDIDEVIIPTAPLYKQILNLYAEENAIEDTIFYLGEALRRGVIDLDVFLKHVRLLSRKQFQLRALMQKARKTAGLSDLY lrsam1-lrsam1-1 3587121 N/A 3587123 unspecified role unspecified role unspecified role unspecified role over-expressed over expressed level over-expressed living cell living cell Q6UWE0:p.Pro707Leu 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 Q6UWE0:p.Leu708_Ser723delinsArgCysAlaAlaArgThrSerProSerAlaSerAlaSerThrThrAlaAlaGluCysCysProProThrTrpAlaTrpSer NP_612370.3:p.Leu708ArgfsTer28 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 N/A 3587123 unspecified role unspecified role unspecified role unspecified role over-expressed over expressed level over-expressed living cell living cell Q6UWE0:p.Pro707Leu 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 Q6UWE0:p.Leu708_Ser723delinsArgCysAlaAlaArgThrSerProSerAlaSerAlaSerThrThrAlaAlaGluCysCysProProThrTrpAlaTrpSer NP_612370.3:p.Leu708ArgfsTer28 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 physical association physical association false false false Figure 2. lrsam1-ube2b-1 3587121 N/A 3587123 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed living cell living cell Q6UWE0:p.Pro707Leu mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false Q6UWE0:p.Cys694Tyr mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false Q6UWE0:p.Gln573Lys 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 Q6UWE0:p.Leu708_Ser723delinsArgCysAlaAlaArgThrSerProSerAlaSerAlaSerThrThrAlaAlaGluCysCysProProThrTrpAlaTrpSer Q6UWE0:p.Leu708ArgfsTer28 mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false N/A 3587124 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed living cell living cell physical association physical association false false false Figure 4. lrsam1-tsg101-6 3587122 N/A 3587123 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed living cell living cell 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 Q6UWE0:p.Leu708_Ser723delinsArgCysAlaAlaArgThrSerProSerAlaSerAlaSerThrThrAlaAlaGluCysCysProProThrTrpAlaTrpSer NP_612370.3:p.Leu708Argfs*28 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 N/A 3587125 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed living cell living cell region gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Figure 3