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/ jones-2006-2 Nck adaptor proteins link nephrin to the actin cytoskeleton of kidney podocytes. human-293 Homo sapiens transformed primary embryonal kidney cells Human 293 Transformed human primary embryonal kidney cells. The Cell type named 293 is synonymous with HEK-293. anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Jones N., Blasutig IM., Eremina V., Ruston JM., Bladt F., Li H., Huang H., Larose L., Li SS., Takano T., Quaggin SE., Pawson T. BioCreative - Critical Assessment of Information Extraction systems in Biology pawson@mshri.on.ca Nature (0028-0836) 2006 Only protein-protein interactions imex curation jones-2006-3 Nck adaptor proteins link nephrin to the actin cytoskeleton of kidney podocytes. mouse-embryonic_fibroblast Mus musculus embryonic fibroblasts embryonic_fibroblast Embryonic fibroblast Fibroblasts taken from an embryonic as opposed to a foetal or adult source. Foetus is defined as the stage at which tissue diferentiation is initiated. Tissue taken from an embryonic as opposed to a foetal or adult source. Embryo is defined as the development stage prior to organ formation. anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Jones N., Blasutig IM., Eremina V., Ruston JM., Bladt F., Li H., Huang H., Larose L., Li SS., Takano T., Quaggin SE., Pawson T. BioCreative - Critical Assessment of Information Extraction systems in Biology Mouse embryonic fibroblasts lacked endogenous Nck1 and Nck2 proteins. pawson@mshri.on.ca Nature (0028-0836) 2006 Only protein-protein interactions imex curation jones-2006-1 Nck adaptor proteins link nephrin to the actin cytoskeleton of kidney podocytes. in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Jones N., Blasutig IM., Eremina V., Ruston JM., Bladt F., Li H., Huang H., Larose L., Li SS., Takano T., Quaggin SE., Pawson T. BioCreative - Critical Assessment of Information Extraction systems in Biology pawson@mshri.on.ca Nature (0028-0836) 2006 Only protein-protein interactions imex curation jones-2006-4 Nck adaptor proteins link nephrin to the actin cytoskeleton of kidney podocytes. mouse-embryonic_fibroblast Mus musculus embryonic fibroblasts embryonic_fibroblast Embryonic fibroblast Fibroblasts taken from an embryonic as opposed to a foetal or adult source. Foetus is defined as the stage at which tissue diferentiation is initiated. Tissue taken from an embryonic as opposed to a foetal or adult source. Embryo is defined as the development stage prior to organ formation. fluorescence imaging fluorescence microscopy fluorescence imaging antibody detection identification by antibody antibody detection Jones N., Blasutig IM., Eremina V., Ruston JM., Bladt F., Li H., Huang H., Larose L., Li SS., Takano T., Quaggin SE., Pawson T. BioCreative - Critical Assessment of Information Extraction systems in Biology pawson@mshri.on.ca Nature (0028-0836) 2006 Only protein-protein interactions imex curation nphn_human Nephrin Renal glomerulus-specific cell adhesion receptor NPHS1 NPHN protein protein human Homo sapiens Human MALGTTLRASLLLLGLLTEGLAQLAIPASVPRGFWALPENLTVVEGASVELRCGVSTPGSAVQWAKDGLLLGPDPRIPGFPRYRLEGDPARGEFHLHIEACDLSDDAEYECQVGRSEMGPELVSPRVILSILVPPKLLLLTPEAGTMVTWVAGQEYVVNCVSGDAKPAPDITILLSGQTISDISANVNEGSQQKLFTVEATARVTPRSSDNRQLLVCEASSPALEAPIKASFTVNVLFPPGPPVIEWPGLDEGHVRAGQSLELPCVARGGNPLATLQWLKNGQPVSTAWGTEHTQAVARSVLVMTVRPEDHGAQLSCEAHNSVSAGTQEHGITLQVTFPPSAIIILGSASQTENKNVTLSCVSKSSRPRVLLRWWLGWRQLLPMEETVMDGLHGGHISMSNLTFLARREDNGLTLTCEAFSEAFTKETFKKSLILNVKYPAQKLWIEGPPEGQKLRAGTRVRLVCLAIGGNPEPSLMWYKDSRTVTESRLPQESRRVHLGSVEKSGSTFSRELVLVTGPSDNQAKFTCKAGQLSASTQLAVQFPPTNVTILANASALRPGDALNLTCVSVSSNPPVNLSWDKEGERLEGVAAPPRRAPFKGSAAARSVLLQVSSRDHGQRVTCRAHSAELRETVSSFYRLNVLYRPEFLGEQVLVVTAVEQGEALLPVSVSANPAPEAFNWTFRGYRLSPAGGPRHRILSSGALHLWNVTRADDGLYQLHCQNSEGTAEARLRLDVHYAPTIRALQDPTEVNVGGSVDIVCTVDANPILPGMFNWERLGEDEEDQSLDDMEKISRGPTGRLRIHHAKLAQAGAYQCIVDNGVAPPARRLLRLVVRFAPQVEHPTPLTKVAAAGDSTSSATLHCRARGVPNIVFTWTKNGVPLDLQDPRYTEHTYHQGGVHSSLLTIANVSAAQDYALFTCTATNALGSDQTNIQLVSISRPDPPSGLKVVSLTPHSVGLEWKPGFDGGLPQRFCIRYEALGTPGFHYVDVVPPQATTFTLTGLQPSTRYRVWLLASNALGDSGLADKGTQLPITTPGLHQPSGEPEDQLPTEPPSGPSGLPLLPVLFALGGLLLLSNASCVGGVLWQRRLRRLAEGISEKTEAGSEEDRVRNEYEESQWTGERDTQSSTVSTTEAEPYYRSLRDFSPQLPPTQEEVSYSRGFTGEDEDMAFPGHLYDEVERTYPPSGAWGPLYDEVQMGPWDLHWPEDTYQDPRGIYDQVAGDLDTLEPDSLPFELRGHLV nck1_human Cytoplasmic protein NCK1 NCK1 NCK NCK adaptor protein 1 SH2/SH3 adaptor protein NCK-alpha protein protein human Homo sapiens Human MAEEVVVVAKFDYVAQQEQELDIKKNERLWLLDDSKSWWRVRNSMNKTGFVPSNYVERKNSARKASIVKNLKDTLGIGKVKRKPSVPDSASPADDSFVDPGERLYDLNMPAYVKFNYMAEREDELSLIKGTKVIVMEKCSDGWWRGSYNGQVGWFPSNYVTEEGDSPLGDHVGSLSEKLAAVVNNLNTGQVLHVVQALYPFSSSNDEELNFEKGDVMDVIEKPENDPEWWKCRKINGMVGLVPKNYVTVMQNNPLTSGLEPSPPQCDYIRPSLTGKFAGNPWYYGKVTRHQAEMALNERGHEGDFLIRDSESSPNDFSVSLKAQGKNKHFKVQLKETVYCIGQRKFSTMEELVEHYKKAPIFTSEQGEKLYLVKHLS nck2_human Cytoplasmic protein NCK2 NCK adaptor protein 2 SH2/SH3 adaptor protein NCK-beta NCK2 GRB4 Growth factor receptor-bound protein 4 protein protein human Homo sapiens Human MTEEVIVIAKWDYTAQQDQELDIKKNERLWLLDDSKTWWRVRNAANRTGYVPSNYVERKNSLKKGSLVKNLKDTLGLGKTRRKTSARDASPTPSTDAEYPANGSGADRIYDLNIPAFVKFAYVAEREDELSLVKGSRVTVMEKCSDGWWRGSYNGQIGWFPSNYVLEEVDEAAAESPSFLSLRKGASLSNGQGSRVLHVVQTLYPFSSVTEEELNFEKGETMEVIEKPENDPEWWKCKNARGQVGLVPKNYVVVLSDGPALHPAHAPQISYTGPSSSGRFAGREWYYGNVTRHQAECALNERGVEGDFLIRDSESSPSDFSVSLKASGKNKHFKVQLVDNVYCIGQRRFHTMDELVEHYKKAPIFTSEHGEKLYLVRALQ wasp_mouse Wiskott-Aldrich syndrome protein homolog Was Wasp protein protein mouse Mus musculus Mouse MNSGPGPVGGRPGGRGGPAVQQNIPSNLLQDHENQRLFELLGRKCWTLATTVVQLYLALPPGAEHWTMEHCGAVCFVKDNPQKSYFIRLYGLQAGRLLWEQELYSQLVYLTPTPFFHTFAGDDCQVGLNFADESEAQAFRALVQEKIQKRNQRQSGERRQLPPPPAPINEERRGGLPPVPPHPGGDHGGPSGGPLSLGLVTVDIQNPDITSSRYRGLPAPGPGPTDKKRSGKKKISKADIGAPSGFKHVSHVGWDPQNGFDVNNLDPDLRSLFSRAGISEAQLTDAETSKLIYDFIEDQGGLEAVRQEMRRQEPLPPPPPPCRGGGGGGGGGGGGGGGGGGQPLRPPVVGSNKGRSGPLPPVPMGGAPPPPTPRGPPPPGRGGPPPPPPPATGRSGPPPPPLPGAGGPPAPPPPPPPPPPPPCPGSGPAPPPLPPTPVSGGSPAPGGGRGALLDQIRQGIQLNKTPGALENSVQQPPAQQSEGLVGALMHVMQKRSRVIHSSDEGEDQTGEDEEDDEWDD nck1-nphs1 Coimmunoprecipitation analysis reveals interaction between Nephrin protein and NCK1 protein 507159 N/A 507163 unspecified role unspecified role bait bait region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false O60500:p.[Tyr1176Phe;Tyr1217Phe] try1176phe-try1217phe mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false O60500:p.[Tyr1193Phe;Tyr1217Phe] try1193phe-try1217phe mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false O60500:p.[Tyr1176Phe;Tyr1193Phe;Tyr1217Phe] try1176phe-try1193phe-try1217phe mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false N/A 507164 unspecified role unspecified role prey prey physical association physical association false false false Figure 2d nck1-nphs1-1 Coimmunoprecipitation analysis reveals interaction between Nephrin protein and NCK1 protein 507159 N/A 507163 unspecified role unspecified role bait bait region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 507164 unspecified role unspecified role prey prey physical association physical association false false false pervandate Figure 2b This interaction was only observed in pervandate stimulated or cells co-transfected with active Src (Proto-oncogene tyrosine-protein kinase). nphs1-nck2 Pulldown analysis reveals interaction between Nephrin protein and Nck2 protein 507160 N/A 507165 unspecified role unspecified role prey prey c terminal flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false N/A 507163 unspecified role unspecified role bait bait region egfp tag enhanced green fluorescent protein tag enhanced green fluorescent protein EGFP enhanced green fluorescent protein EGFP egfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false c terminal Intracellular domain sufficient to bind sufficient binding region sufficient to bind range range range range false region Extracellular and transmembrane domain of CD16 and CD7 proteins tag tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false O60500:p.[Tyr1176Phe;Tyr1193Phe;Tyr1217Phe] try1176phe-try1193phe-try1217phe mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false Figure 4a The nephrin protein was phosphorylated and tagged with CD16 and CD7 extracellular and transmembrane domains. Interaction between these proteins was increased when anti-DD16 antibody was used in the assay. The coordinates of the intracellular region of the nephrin protein were not given in the text and were determined from the annotation available in the corresponding UniProt accession entry. nphs1-wasp Pulldown analysis reveals interaction between Nephrin protein and WASP protein 507160 N/A 507166 unspecified role unspecified role prey prey c terminal flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false N/A 507163 unspecified role unspecified role bait bait region egfp tag enhanced green fluorescent protein tag enhanced green fluorescent protein EGFP enhanced green fluorescent protein EGFP egfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false c terminal Intracellular domain sufficient to bind sufficient binding region sufficient to bind range range range range false region Extracellular and transmembrane domain of CD16 and CD7 proteins tag tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false O60500:p.[Tyr1176Phe;Tyr1193Phe;Tyr1217Phe] try1176phe-try1193phe-try1217phe mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false Figure 4a The nephrin protein was phosphorylated and tagged with CD16 and CD7 extracellular and transmembrane domains. Interaction between these proteins was increased when anti-DD16 antibody was used in the assay. The coordinates of the intracellular region of the nephrin protein were not given in the text and were determined from the annotation available in the corresponding UniProt accession entry. nphs1-nck1 Pulldown analysis reveals interaction between Nephrin protein and NCK1 protein 507161 N/A 507163 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 ecoli Escherichia coli (strain K12) N/A 507164 unspecified role unspecified role bait bait c terminal sufficient to bind sufficient binding region sufficient to bind range range range range false 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 false ecoli Escherichia coli (strain K12) physical association physical association false false false Figure 2a The co-ordinates of the SH2 domain used in this study were not given and are taken from UniProt annotation of the protein. This interaction was only observed in pervandate stimulated or cells co-transfected with active Src (Proto-oncogene tyrosine-protein kinase). nphs1-nck2-1 Colocalisation analysis reveals interaction between Nephrin protein and Nck2 protein 507162 N/A 507165 unspecified role unspecified role neutral component neutral component c terminal flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false N/A 507163 unspecified role unspecified role neutral component neutral component region egfp tag enhanced green fluorescent protein tag enhanced green fluorescent protein EGFP enhanced green fluorescent protein EGFP egfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false c terminal Intracellular domain sufficient to bind sufficient binding region sufficient to bind range range range range false region Extracellular and transmembrane domain of CD16 and CD7 proteins tag tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false O60500:p.[Tyr1176Phe;Tyr1193Phe;Tyr1217Phe] try1176phe-try1193phe-try1217phe mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false colocalization colocalization false false false Figure 4c Figure 4d The nephrin protein was phosphorylated and tagged with CD16 and CD7 extracellular and transmembrane domains. The coordinates of the intracellular region of the nephrin protein were not given in the text and were determined from the annotation available in the corresponding UniProt accession entry.