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/ urushitani-2006-2 Chromogranin-mediated secretion of mutant superoxide dismutase proteins linked to amyotrophic lateral sclerosis. mouse-neuro_2_a Mus musculus albino neuroblastoma cell line neuro 2 a (N2a) neuro_2_a Mouse Albino neuroblastoma neuro 2 a cell line anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Urushitani M., Sik A., Sakurai T., Nukina N., Takahashi R., Julien JP. BioCreative - Critical Assessment of Information Extraction systems in Biology julien@crchul.ulaval.ca Nat. Neurosci. (1097-6256) 2006 Only protein-protein interactions imex curation Synapse - Interactions of proteins with an established role in the presynapse. The gly93ala, ala4val,gly37arg and gly85arg SOD1 mutations have been entered using sequence as stated in UniProt ID= P00441, as gly94ala, ala5val,gly38arg and gly86arg; assuming the N-terminal methionine was not included in the numbering used in this publication. Mouse cDNA library from transgenic mouse transformed with mutant SOD (G39A) protein. urushitani-2006-5 Chromogranin-mediated secretion of mutant superoxide dismutase proteins linked to amyotrophic lateral sclerosis. mouse Mus musculus Mouse anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Urushitani M., Sik A., Sakurai T., Nukina N., Takahashi R., Julien JP. BioCreative - Critical Assessment of Information Extraction systems in Biology Cells from spinal neurons of transgenic (expressing SOD1 gly37arg) or wild type mice were used in this assay. julien@crchul.ulaval.ca Mouse cDNA library from transgenic mouse transformed with mutant SOD (G39A) protein. Nat. Neurosci. (1097-6256) 2006 Only protein-protein interactions imex curation Synapse - Interactions of proteins with an established role in the presynapse. The gly93ala, ala4val,gly37arg and gly85arg SOD1 mutations have been entered using sequence as stated in UniProt ID= P00441, as gly94ala, ala5val,gly38arg and gly86arg; assuming the N-terminal methionine was not included in the numbering used in this publication. urushitani-2006-1 Chromogranin-mediated secretion of mutant superoxide dismutase proteins linked to amyotrophic lateral sclerosis. 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 Urushitani M., Sik A., Sakurai T., Nukina N., Takahashi R., Julien JP. BioCreative - Critical Assessment of Information Extraction systems in Biology julien@crchul.ulaval.ca Mouse cDNA library from transgenic mouse spinal cord cell, carrying human mutant SOD (G39A) protein. Nat. Neurosci. (1097-6256) 2006 Only protein-protein interactions imex curation Synapse - Interactions of proteins with an established role in the presynapse. The gly93ala, ala4val,gly37arg and gly85arg SOD1 mutations have been entered using sequence as stated in UniProt ID= P00441, as gly94ala, ala5val,gly38arg and gly86arg; assuming the N-terminal methionine was not included in the numbering used in this publication. Mouse cDNA library from transgenic mouse transformed with mutant SOD (G39A) protein. urushitani-2006-3 Chromogranin-mediated secretion of mutant superoxide dismutase proteins linked to amyotrophic lateral sclerosis. mouse-neuro_2_a Mus musculus albino neuroblastoma cell line neuro 2 a (N2a) neuro_2_a Mouse Albino neuroblastoma neuro 2 a cell line fluorescence imaging fluorescence microscopy fluorescence imaging antibody detection identification by antibody antibody detection Urushitani M., Sik A., Sakurai T., Nukina N., Takahashi R., Julien JP. BioCreative - Critical Assessment of Information Extraction systems in Biology Cells from spinal neurons of transgenic (expressing SOD1 gly37arg) or wild type mice were used in this assay. julien@crchul.ulaval.ca Mouse cDNA library from transgenic mouse transformed with mutant SOD (G39A) protein. Nat. Neurosci. (1097-6256) 2006 Only protein-protein interactions imex curation Synapse - Interactions of proteins with an established role in the presynapse. The gly93ala, ala4val,gly37arg and gly85arg SOD1 mutations have been entered using sequence as stated in UniProt ID= P00441, as gly94ala, ala5val,gly38arg and gly86arg; assuming the N-terminal methionine was not included in the numbering used in this publication. urushitani-2006-4 Chromogranin-mediated secretion of mutant superoxide dismutase proteins linked to amyotrophic lateral sclerosis. mouse-neuron Mus musculus neuronal cell neuron Neuron [Neuronal cell; Neural cell fluorescence imaging fluorescence microscopy fluorescence imaging antibody detection identification by antibody antibody detection Urushitani M., Sik A., Sakurai T., Nukina N., Takahashi R., Julien JP. BioCreative - Critical Assessment of Information Extraction systems in Biology Cells from spinal neurons of transgenic (expressing SOD1 gly37arg) or wild type mice were used in this assay. julien@crchul.ulaval.ca Mouse cDNA library from transgenic mouse transformed with mutant SOD (G39A) protein. Nat. Neurosci. (1097-6256) 2006 Only protein-protein interactions imex curation Synapse - Interactions of proteins with an established role in the presynapse. The gly93ala, ala4val,gly37arg and gly85arg SOD1 mutations have been entered using sequence as stated in UniProt ID= P00441, as gly94ala, ala5val,gly38arg and gly86arg; assuming the N-terminal methionine was not included in the numbering used in this publication. urushitani-2006-6 Chromogranin-mediated secretion of mutant superoxide dismutase proteins linked to amyotrophic lateral sclerosis. mouse Mus musculus Mouse density sedimentation cosedimentation through density gradient density sedimentation western blot western blot Immuno blot Immuno blot Urushitani M., Sik A., Sakurai T., Nukina N., Takahashi R., Julien JP. BioCreative - Critical Assessment of Information Extraction systems in Biology Cells from spinal neurons of transgenic (expressing SOD1 gly37arg) or wild type mice were used in this assay. julien@crchul.ulaval.ca Mouse cDNA library from transgenic mouse transformed with mutant SOD (G39A) protein. Nat. Neurosci. (1097-6256) 2006 Only protein-protein interactions imex curation Synapse - Interactions of proteins with an established role in the presynapse. The gly93ala, ala4val,gly37arg and gly85arg SOD1 mutations have been entered using sequence as stated in UniProt ID= P00441, as gly94ala, ala5val,gly38arg and gly86arg; assuming the N-terminal methionine was not included in the numbering used in this publication. urushitani-2006-7 Chromogranin-mediated secretion of mutant superoxide dismutase proteins linked to amyotrophic lateral sclerosis. mouse Mus musculus Mouse electron microscopy electron microscopy Electron crystallography Electron cryomicroscopy Electron crystallography Electron cryomicroscopy antibody detection identification by antibody antibody detection Urushitani M., Sik A., Sakurai T., Nukina N., Takahashi R., Julien JP. BioCreative - Critical Assessment of Information Extraction systems in Biology Cells from spinal neurons of transgenic (expressing SOD1 gly37arg) or wild type mice were used in this assay. julien@crchul.ulaval.ca Mouse cDNA library from transgenic mouse transformed with mutant SOD (G39A) protein. Nat. Neurosci. (1097-6256) 2006 Only protein-protein interactions imex curation Synapse - Interactions of proteins with an established role in the presynapse. The gly93ala, ala4val,gly37arg and gly85arg SOD1 mutations have been entered using sequence as stated in UniProt ID= P00441, as gly94ala, ala5val,gly38arg and gly86arg; assuming the N-terminal methionine was not included in the numbering used in this publication. sodc_human Superoxide dismutase [Cu-Zn] Superoxide dismutase 1 SOD1 protein protein human Homo sapiens Human MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ scg1_mouse Secretogranin-1 Secretogranin I Chromogranin-B Chgb Scg1 Scg-1 protein protein mouse Mus musculus Mouse MQPAMLLGLLGAAALAAVSSAPVDNRDHNEEMVTRCIIEVLSNALSKSSVPTITPECRQVLKKSGKEVKGEEKGENQNSKFEVRLLRDPADASGTRWASSREDAGAPVEDSQGQTKVGNEKWTEGGGHSREGVDDQESLRPSNQQASKEAKIYHSEERVGKEREKEEGKIYPMGEHREDAGEEKKHIEDSGEKPNTFSNKRSEASAKKKDESVARADAHSMELEEKTHSREQSSQESGEETRRQEKPQELTDQDQSQEESQEGEEGEEGEEGEEGEEDSASEVTKRRPRHHHGRSGSNKSSYEGHPLSEERRPSPKESKEADVATVRLGEKRSHHLAHYRASEEEPEYGEESRSYRGLQYRGRGSEEDRAPRPRSEESQEREYKRNHPDSELESTANRHGEETEEERSYEGANGRQHRGRGREPGAHSALDTREEKRLLDEGHYPVRESPIDTAKRYPQSKWQEQEKNYLNYGEEGDQGRWWQQEEQLGPEESREEVRFPDRQYEPYPITEKRKRLGALFNPYFDPLQWKNSDFEKRGNPDDSFLEDEGEDRNGVTLTEKNSFPEYNYDWWERRPFSEDVNWGYEKRSFARAPQLDLKRQYDGVAELDQLLHYRKKADEFPDFYDSEEQMGPHQEANDEKARADQRVLTAEEKKELENLAAMDLELQKIAEKFSQRG cmga_mouse Chromogranin-A Chga protein protein mouse Mus musculus Mouse MRSTAVLALLLCAGQVFALPVNSPMTKGDTKVMKCVLEVISDSLSKPSPMPVSPECLETLQGDERILSILRHQNLLKELQDLALQGAKERAQQPLKQQQPPKQQQQQQQQQQQEQQHSSFEDELSEVFENQSPDAKHRDAAAEVPSRDTMEKRKDSDKGQQDGFEATTEGPRPQAFPEPNQESPMMGDSESPGEDTATNTQSPTSLPSQEHVDPQATGDSERGLSAQQQARKAKQEEKEEEEEEEAVAREKAGPEEVPTAASSSHFHAGYKAIQKDDGQSDSQAVDGDGKTEASEALPSEGKGELEHSQQEEDGEEAMVGTPQGLFPQGGKGRELEHKQEEEEEEEERLSREWEDKRWSRMDQLAKELTAEKRLEGEDDPDRSMKLSFRTRAYGFRDPGPQLRRGWRPSSREDSVEARSDFEEKKEEEGSANRRAEDQELESLSAIEAELEKVAHQLQALRRG tgon1_mouse Trans-Golgi network integral membrane protein 1 TGN38A Tgoln1 Ttgn1 protein protein mouse Mus musculus Mouse MRFQVALLLLSVAVARALPSVYKRDADSGDSQNPPNQPSKQSSTPLPSSNQVKTTRPTDGQGQKSDKKDQDKTTLAAVSSKAESGPRTAATDHSLGDSRRQPEKTDAELNETARPLSPVNPKLEKSDQSSTEDSGKPTGGNSGKPTGGDSGKPTEAGSNKATEDDSGKSTKVDLDKPTSKISPDTETSKTDKVQPTEKGQKPTLTSKTESGETLAGDSDFSLKPEKGDKSSEPTEDVETKEIEEGDTEPEEGSPLEEENEKVPGPSSSENQEGTLTDSMKNEKDDLYKDSSGNTSAESSHFFAYLVTAAVLVAVLYIAYHNKRKIIAFALEGKRSKVTRRPKASDYQRLNLKL stx1a_mouse Syntaxin-1A Stx1a Neuron-specific antigen HPC-1 protein protein mouse Mus musculus Mouse MKDRTQELRTAKDSDDDDDVTVTVDRDRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSAILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQHSTLSRKFVEVMSEYNATQSDYRERCKGRIQRQLEITGRTTTSEELEDMLESGNPAIFASGIIMDSSISKQALSEIETRHSEIIKLETSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVSDTKKAVKYQSKARRKKIMIIICCVILGIIIASTIGGIFG sod1-cgb-2 Coimmunoprecipitation assay reveals interaction between SOD1 protein and Cgb protein 505669 N/A 505676 unspecified role unspecified role bait bait P00441:p.Gly94Ala mutation mutation certain certain sequence position certain certain certain sequence position certain false n-terminal flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false P00441:p.Gly86Arg mutation mutation certain certain sequence position certain certain certain sequence position certain false P00441:p.Ala5Val mutation mutation certain certain sequence position certain certain certain sequence position certain false N/A 505677 unspecified role unspecified role prey prey c terminal ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope 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 Figure 1a sod1-cga-1 Coimmunoprecipitation assay reveals interaction between SOD1 protein and CgA protein 505669 N/A 505678 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 false N/A 505676 unspecified role unspecified role bait bait P00441:p.Gly94Ala mutation mutation certain certain sequence position certain certain certain sequence position certain false n-terminal flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false P00441:p.Gly86Arg mutation mutation certain certain sequence position certain certain certain sequence position certain false P00441:p.Ala5Val mutation mutation certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false Figure 1b sod1-cgb-3 Coimmunoprecipitation assay reveals interaction between SOD1 protein and Cgb protein 505669 N/A 505677 unspecified role unspecified role prey prey c terminal ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false N/A 505676 unspecified role unspecified role bait bait n-terminal flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false region required to bind necessary binding region required to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false Figure 1c sod1-tgn38a Coimmunoprecipitation assay reveals interaction between SOD1 protein and TGN38 protein 505670 N/A 505676 unspecified role unspecified role prey prey P00441:p.Gly38Arg mutation increasing mutation increasing interaction mutation increasing certain certain sequence position certain certain certain sequence position certain false P00441:p.Gly94Ala mutation increasing mutation increasing interaction mutation increasing certain certain sequence position certain certain certain sequence position certain false N/A 505679 unspecified role unspecified role bait bait physical association physical association false false false Figure 1a Interaction between mutated forms of SOD1 with TN38 protein was much greater than with SOD1 wild type and TN38 protein. cga-sod1 Coimmunoprecipitation assay reveals interaction between CgA protein and SOD1 protein 505670 N/A 505676 unspecified role unspecified role prey prey P00441:p.Gly94Ala mutation mutation certain certain sequence position certain certain certain sequence position certain false P00441:p.Gly38Arg mutation mutation certain certain sequence position certain certain certain sequence position certain false N/A 505678 unspecified role unspecified role bait bait physical association physical association false false false Figure 3d cgb-sod1-1 Coimmunoprecipitation assay reveals interaction between CgB protein and SOD1 protein 505670 N/A 505677 unspecified role unspecified role bait bait N/A 505676 unspecified role unspecified role prey prey P00441:p.Gly38Arg mutation mutation certain certain sequence position certain certain certain sequence position certain false P00441:p.Gly94Ala mutation mutation certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false Figure 3d sod1-cgb-1 Yeast two hybrid assay reveals interaction between SOD1 protein and Cgb protein 505671 N/A 505677 unspecified role unspecified role prey prey N/A 505676 unspecified role unspecified role bait bait P00441:p.Gly94Ala mutation mutation certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false The authors state that a 76 amino acid region of the CgB protein interacted with the mutant SOD1 bait, but do not specify its coordinates. cgb-sod1-2 Yeast two hybrid assay reveals interaction between SOD1 protein and Cgb protein 505671 N/A 505676 unspecified role unspecified role prey prey P00441:p.Gly94Ala mutation mutation certain certain sequence position certain certain certain sequence position certain false N/A 505677 unspecified role unspecified role bait bait physical association physical association false false false sod1-cgb-4 Colocalisation of SOD1 protein and CgB protein 505672 N/A 505676 unspecified role unspecified role neutral component neutral component P00441:p.Gly86Arg mutation mutation certain certain sequence position certain certain certain sequence position certain false P00441:p.Gly94Ala mutation mutation certain certain sequence position certain certain certain sequence position certain false N/A 505677 unspecified role unspecified role neutral component neutral component c terminal egfp tag enhanced green fluorescent protein tag enhanced green fluorescent protein EGFP enhanced green fluorescent protein EGFP egfp tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false colocalization colocalization false false false Figure 1j A total colocalisation of mutant SOD and CgB proteins was observed in roughly 10 percent of transfected cells. sod1-cgb-cga Colocalisation of SOD1 protein, CgA protein and CgB protein 505673 N/A 505678 unspecified role unspecified role neutral component neutral component N/A 505676 unspecified role unspecified role neutral component neutral component P00441:p.Gly38Arg mutation mutation certain certain sequence position certain certain certain sequence position certain false N/A 505677 unspecified role unspecified role neutral component neutral component colocalization colocalization false false false Figure 2c Partial colocalisation of mutant SOD1 with CgA and CgB was detected in in irregular and large vesicular struuctures of spinal neurons from G37R transgenic mice sod1-cgb-cga-1 Cosedimentation of SOD1, CgA , CgB , synaptophysin, syntaxin1 proteins 505674 N/A 505678 unspecified role unspecified role neutral component neutral component N/A 505680 unspecified role unspecified role neutral component neutral component N/A 505676 unspecified role unspecified role neutral component neutral component P00441:p.Gly38Arg mutation mutation certain certain sequence position certain certain certain sequence position certain false N/A 505677 unspecified role unspecified role neutral component neutral component physical association physical association false false false Figure 3b Could not idetify adaptin protein. sod1-cgb-cga-2 Colocalisation of SOD1 protein , CgA protein and CgB protein 505675 N/A 505678 unspecified role unspecified role neutral component neutral component N/A 505677 unspecified role unspecified role neutral component neutral component N/A 505676 unspecified role unspecified role neutral component neutral component P00441:p.Gly38Arg mutation mutation certain certain sequence position certain certain certain sequence position certain false colocalization colocalization false false false No significant colocalisation with wild type (endogenous) SOD1 and chromogranins was observed in this study. Figure 4