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/ Involvement of Ymer in suppression of NF-kappaB activation by regulated interaction with lysine-63-linked polyubiquitin chain. Involvement of Ymer in suppression of NF-kappaB activation by regulated interaction with lysine-63-linked polyubiquitin chain. Biochim. Biophys. Acta (0006-3002) 2007 Bohgaki M., Tsukiyama T., Nakajima A., Maruyama S., Watanabe M., Koike T., Hatakeyama S. Cancer - Interactions investigated in the context of cancer hatas@med.hokudai.ac.jp 14-May-2008: Contacted by JYOTI. A human B cell Matchmaker cDNA library (Clontech) was used. davet human-hela Homo sapiens epitheloid cervix carcinoma cells Human hela Human epitheloid cervix carcinoma HeLa cells derivation: cervix; epithelial; adenocarcinoma ATCC no:CCL-2 fluorescence imaging fluorescence microscopy fluorescence imaging polyclonal immunost polyclonal antibody immunostaining polyclonal immunost Bohgaki M., Tsukiyama T., Nakajima A., Maruyama S., Watanabe M., Koike T., Hatakeyama S. Cancer - Interactions investigated in the context of cancer hatas@med.hokudai.ac.jp Accepted 2008-MAY-30 by DAVET. 14-May-2008: Contacted by JYOTI. A human B cell Matchmaker cDNA library (Clontech) was used. Biochim. Biophys. Acta (0006-3002) 2007 davet Involvement of Ymer in suppression of NF-kappaB activation by regulated interaction with lysine-63-linked polyubiquitin chain. Involvement of Ymer in suppression of NF-kappaB activation by regulated interaction with lysine-63-linked polyubiquitin chain. Biochim. Biophys. Acta (0006-3002) 2007 Bohgaki M., Tsukiyama T., Nakajima A., Maruyama S., Watanabe M., Koike T., Hatakeyama S. Cancer - Interactions investigated in the context of cancer hatas@med.hokudai.ac.jp 14-May-2008: Contacted by JYOTI. A human B cell Matchmaker cDNA library (Clontech) was used. davet human-jurkat Homo sapiens jurkat Human T cell leukemia anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Bohgaki M., Tsukiyama T., Nakajima A., Maruyama S., Watanabe M., Koike T., Hatakeyama S. Cancer - Interactions investigated in the context of cancer hatas@med.hokudai.ac.jp Accepted 2008-MAY-30 by DAVET. 14-May-2008: Contacted by JYOTI. A human B cell Matchmaker cDNA library (Clontech) was used. Biochim. Biophys. Acta (0006-3002) 2007 davet Involvement of Ymer in suppression of NF-kappaB activation by regulated interaction with lysine-63-linked polyubiquitin chain. Involvement of Ymer in suppression of NF-kappaB activation by regulated interaction with lysine-63-linked polyubiquitin chain. Biochim. Biophys. Acta (0006-3002) 2007 Bohgaki M., Tsukiyama T., Nakajima A., Maruyama S., Watanabe M., Koike T., Hatakeyama S. Cancer - Interactions investigated in the context of cancer hatas@med.hokudai.ac.jp 14-May-2008: Contacted by JYOTI. A human B cell Matchmaker cDNA library (Clontech) was used. davet 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 Bohgaki M., Tsukiyama T., Nakajima A., Maruyama S., Watanabe M., Koike T., Hatakeyama S. Cancer - Interactions investigated in the context of cancer hatas@med.hokudai.ac.jp Accepted 2008-MAY-30 by DAVET. 14-May-2008: Contacted by JYOTI. A human B cell Matchmaker cDNA library (Clontech) was used. Biochim. Biophys. Acta (0006-3002) 2007 davet Involvement of Ymer in suppression of NF-kappaB activation by regulated interaction with lysine-63-linked polyubiquitin chain. Involvement of Ymer in suppression of NF-kappaB activation by regulated interaction with lysine-63-linked polyubiquitin chain. Biochim. Biophys. Acta (0006-3002) 2007 Bohgaki M., Tsukiyama T., Nakajima A., Maruyama S., Watanabe M., Koike T., Hatakeyama S. Cancer - Interactions investigated in the context of cancer hatas@med.hokudai.ac.jp 14-May-2008: Contacted by JYOTI. A human B cell Matchmaker cDNA library (Clontech) was used. davet 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 nucleotide sequence nucleotide sequence identification sequence cloning sequence cloning nucleotide sequence Bohgaki M., Tsukiyama T., Nakajima A., Maruyama S., Watanabe M., Koike T., Hatakeyama S. Cancer - Interactions investigated in the context of cancer hatas@med.hokudai.ac.jp Accepted 2008-MAY-30 by DAVET. 14-May-2008: Contacted by JYOTI. A human B cell Matchmaker cDNA library (Clontech) was used. Biochim. Biophys. Acta (0006-3002) 2007 davet Involvement of Ymer in suppression of NF-kappaB activation by regulated interaction with lysine-63-linked polyubiquitin chain. Involvement of Ymer in suppression of NF-kappaB activation by regulated interaction with lysine-63-linked polyubiquitin chain. Biochim. Biophys. Acta (0006-3002) 2007 Bohgaki M., Tsukiyama T., Nakajima A., Maruyama S., Watanabe M., Koike T., Hatakeyama S. Cancer - Interactions investigated in the context of cancer hatas@med.hokudai.ac.jp 14-May-2008: Contacted by JYOTI. A human B cell Matchmaker cDNA library (Clontech) was used. davet in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Bohgaki M., Tsukiyama T., Nakajima A., Maruyama S., Watanabe M., Koike T., Hatakeyama S. Cancer - Interactions investigated in the context of cancer hatas@med.hokudai.ac.jp Accepted 2008-MAY-30 by DAVET. 14-May-2008: Contacted by JYOTI. A human B cell Matchmaker cDNA library (Clontech) was used. Biochim. Biophys. Acta (0006-3002) 2007 davet ccd50_human Coiled-coil domain-containing protein 50 Protein Ymer CCDC50 C3orf6 protein protein human Homo sapiens Human MAEVSIDQSKLPGVKEVCRDFAVLEDHTLAHSLQEQEIEHHLASNVQRNRLVQHDLQVAKQLQEEDLKAQAQLQKRYKDLEQQDCEIAQEIQEKLAIEAERRRIQEKKDEDIARLLQEKELQEEKKRKKHFPEFPATRAYADSYYYEDGGMKPRVMKEAVSTPSRMAHRDQEWYDAEIARKLQEEELLATQVDMRAAQVAQDEEIARLLMAEEKKAYKKAKEREKSSLDKRKQDPEWKPKTAKAANSKSKESDEPHHSKNERPARPPPPIMTDGEDADYTHFTNQQSSTRHFSKSESSHKGFHYKH 3E935B62225CC93F tnip2_human TNFAIP3-interacting protein 2 TNIP2 ABIN2 FLIP1 Fetal liver LKB1-interacting protein A20-binding inhibitor of NF-kappa-B activation 2 protein protein human Homo sapiens Human MSRDPGSGGWEEAPRAAAALCTLYHEAGQRLRRLQDQLAARDALIARLRARLAALEGDAAPSLVDALLEQVARFREQLRRQEGGAAEAQMRQEIERLTERLEEKEREMQQLLSQPQHEREKEVVLLRRSMAEGERARAASDVLCRSLANETHQLRRTLTATAHMCQHLAKCLDERQHAQRNVGERSPDQSEHTDGHTSVQSVIEKLQEENRLLKQKVTHVEDLNAKWQRYNASRDEYVRGLHAQLRGLQIPHEPELMRKEISRLNRQLEEKINDCAEVKQELAASRTARDAALERVQMLEQQILAYKDDFMSERADRERAQSRIQELEEKVASLLHQVSWRQDSREPDAGRIHAGSKTAKYLAADALELMVPGGWRPGTGSQQPEPPAEGGHPGAAQRGQGDLQCPHCLQCFSDEQGEELLRHVAECCQ 0F6B049C2B3483DC otu7b_human OTU domain-containing protein 7B Zinc finger protein Cezanne Zinc finger A20 domain-containing protein 1 Cellular zinc finger anti-NF-kappa-B protein OTUD7B ZA20D1 protein protein human Homo sapiens Human MTLDMDAVLSDFVRSTGAEPGLARDLLEGKNWDVNAALSDFEQLRQVHAGNLPPSFSEGSGGSRTPEKGFSDREPTRPPRPILQRQDDIVQEKRLSRGISHASSSIVSLARSHVSSNGGGGGSNEHPLEMPICAFQLPDLTVYNEDFRSFIERDLIEQSMLVALEQAGRLNWWVSVDPTSQRLLPLATTGDGNCLLHAASLGMWGFHDRDLMLRKALYALMEKGVEKEALKRRWRWQQTQQNKESGLVYTEDEWQKEWNELIKLASSEPRMHLGTNGANCGGVESSEEPVYESLEEFHVFVLAHVLRRPIVVVADTMLRDSGGEAFAPIPFGGIYLPLEVPASQCHRSPLVLAYDQAHFSALVSMEQKENTKEQAVIPLTDSEYKLLPLHFAVDPGKGWEWGKDDSDNVRLASVILSLEVKLHLLHSYMNVKWIPLSSDAQAPLAQPESPTASAGDEPRSTPESGDSDKESVGSSSTSNEGGRRKEKSKRDREKDKKRADSVANKLGSFGKTLGSKLKKNMGGLMHSKGSKPGGVGTGLGGSSGTETLEKKKKNSLKSWKGGKEEAAGDGPVSEKPPAESVGNGGSKYSQEVMQSLSILRTAMQGEGKFIFVGTLKMGHRHQYQEEMIQRYLSDAEERFLAEQKQKEAERKIMNGGIGGGPPPAKKPEPDAREEQPTGPPAESRAMAFSTGYPGDFTIPRPSGGGVHCQEPRRQLAGGPCVGGLPPYATFPRQCPPGRPYPHQDSIPSLEPGSHSKDGLHRGALLPPPYRVADSYSNGYREPPEPDGWAGGLRGLPPTQTKCKQPNCSFYGHPETNNFCSCCYREELRRREREPDGELLVHRF DIP protein Q6GQQ9 original sequence version: 96 6D386C864B12EE57 ubb_human Polyubiquitin-B UBB protein protein human Homo sapiens Human MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGC 33011162F1C48BB1 ripk1_human Receptor-interacting serine/threonine-protein kinase 1 RIPK1 RIP Cell death protein RIP RIP1 Receptor-interacting protein 1 protein protein human Homo sapiens Human MQPDMSLNVIKMKSSDFLESAELDSGGFGKVSLCFHRTQGLMIMKTVYKGPNCIEHNEALLEEAKMMNRLRHSRVVKLLGVIIEEGKYSLVMEYMEKGNLMHVLKAEMSTPLSVKGRIILEIIEGMCYLHGKGVIHKDLKPENILVDNDFHIKIADLGLASFKMWSKLNNEEHNELREVDGTAKKNGGTLYYMAPEHLNDVNAKPTEKSDVYSFAVVLWAIFANKEPYENAICEQQLIMCIKSGNRPDVDDITEYCPREIISLMKLCWEANPEARPTFPGIEEKFRPFYLSQLEESVEEDVKSLKKEYSNENAVVKRMQSLQLDCVAVPSSRSNSATEQPGSLHSSQGLGMGPVEESWFAPSLEHPQEENEPSLQSKLQDEANYHLYGSRMDRQTKQQPRQNVAYNREEERRRRVSHDPFAQQRPYENFQNTEGKGTAYSSAASHGNAVHQPSGLTSQPQVLYQNNGLYSSHGFGTRPLDPGTAGPRVWYRPIPSHMPSLHNIPVPETNYLGNTPTMPFSSLPPTDESIKYTIYNSTGIQIGAYNYMEIGGTSSSLLDSTNTNFKEEPAAKYQAIFDNTTSLTDKHLDPIRENLGKHWKNCARKLGFTQSQIDEIDHDYERDGLKEKVYQMLQKWVMREGIKGATVGKLAQALHQCSRIDLLSSLIYVSQN DIP protein Q13546 original sequence version: 158 DIP protein Q13546-1 original sequence version: 140 DIP protein Q13546 original sequence version: 146 DIP protein Q13546-1 original sequence version: 146 DIP protein Q13546 original sequence version: 134 DIP protein Q13546 original sequence version: 109 976E2428D525A9B2 1433b_human 14-3-3 protein beta/alpha YWHAB Protein kinase C inhibitor protein 1 Protein 1054 protein protein human Homo sapiens Human MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN DIP protein P31946 original sequence version: 171 DIP protein P31946 original sequence version: 97 DIP protein P31946 original sequence version: 119 DIP protein P31946 original sequence version: 122 DIP protein P31946 original sequence version: 180 6BE1A9BF97468017 otud7b-ccdc50 4 6 unspecified role unspecified role prey prey 8 unspecified role unspecified role bait bait physical association physical association Using a yeast two-hybrid system to search for proteins interacting with A20, we identified one novel binding protein, Ymer. PREY gene AJ416916 otud7b-ywhab 4 8 unspecified role unspecified role bait bait 11 unspecified role unspecified role prey prey physical association physical association we constructed a fulllength A20 cDNA in pBTM116 for yeast two-hybrid screening using a human B cell cDNA library. Sixty positive clones were isolated on Leu-Trp-His-deficient medium from 2.5 106 transformants. Several previously reported proteins including, 14-3-3, 14-3-3 and ABIN-1/2 [20,21], and one novel protein, Ymer (accession number: AJ416916), were isolated. otud7b-tnip2 4 8 unspecified role unspecified role bait bait 7 unspecified role unspecified role prey prey physical association physical association we constructed a fulllength A20 cDNA in pBTM116 for yeast two-hybrid screening using a human B cell cDNA library. Sixty positive clones were isolated on Leu-Trp-His-deficient medium from 2.5 106 transformants. Several previously reported proteins including, 14-3-3, 14-3-3 and ABIN-1/2 [20,21], and one novel protein, Ymer (accession number: AJ416916), were isolated. ccdc50-otud7b-1 3 6 unspecified role unspecified role bait bait region required to bind necessary binding region required to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain 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 8 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 region required to bind necessary binding region required to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain physical association physical association BAIT gene AJ416916 Immunoprecipitation and immunoblot analysis revealed that HA-tagged A20 interacted with FLAG-tagged Ymer 1 A, D, E, F, 3 A Q6GQQ9; Q8IVM0 transfection ccdc50-otud7b 2 6 unspecified role unspecified role bait bait 8 unspecified role unspecified role prey prey physical association physical association BAIT gene AJ416916 We also verified interaction between endogenous A20 and endogenous Ymer by anti-A20 and anti-Ymer antibodies 1 B ccdc50-otud7b-2 1 6 unspecified role unspecified role neutral component neutral component 8 unspecified role unspecified role neutral component neutral component colocalization colocalization Q8IVM0 gene AJ416916 1 C Immunofluorescence staining showed that both A20 and Ymer partially localized in the cytosol ccdc50-rps27a 4 6 unspecified role unspecified role bait bait 9 unspecified role unspecified role prey prey physical association physical association BAIT gene AJ416916 To identify proteins binding to Ymer, we performed yeast two-hybrid screening using full-length human Ymer cDNA as a bait. Eight positive cDNA clones isolated from 1.8 106 transformants were several types of ubiquitin cDNA. ccdc50-rps27a-1 5 6 unspecified role unspecified role bait bait region required to bind necessary binding region required to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain Q8IVM0:p.Leu116Pro mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain L P Wed May 02 15:40:48 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'leu116pro' Tue Jun 30 19:52:18 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Leu116Pro' region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined ecoli Escherichia coli (strain K12) 9 unspecified role unspecified role prey prey physical association physical association BAIT gene AJ416916 2 An in vitro pull-down assay also verified that K63-linked polyubiquitin chains bound the wild type of Ymer otud7b-rps27a 5 6 unspecified role unspecified role ancillary ancillary 9 unspecified role unspecified role prey prey 8 unspecified role unspecified role bait bait association association ANCILLARY gene AJ416916 3 B The in vitro binding assay showed that A20 alone associates with the K63 polyubiquitin chain and that the association is enhanced in the presence of Ymer OTUD7b (A20) associates with K63 polyubiquItin chain. This interaction is enhanced by the presence of CCDC50 (Ymer), which suggests CCDC50 may act as a scaffold between the two. ccdc50-ripk1 3 6 unspecified role unspecified role bait bait region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 10 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 physical association physical association BAIT gene AJ416916 Q13546; Q8IVM0 transfection 4 A, D The immunoprecipitates with antibodies to Ymer contained RIP1 ccdc50-ripk1-1 5 10 unspecified role unspecified role prey prey 6 unspecified role unspecified role bait bait region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined ecoli Escherichia coli (strain K12) physical association physical association BAIT gene AJ416916 4 F An in vitro binding assay showed that Ymer interacts with RIP1, regardless of whether RIP1 is ubiquitinated or not CCDC50 (Ymer) interacts with RIP1 whether RIP1 is ubiquitinated or not.