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/ The diabetes susceptibility gene Clec16a regulates mitophagy. The diabetes susceptibility gene Clec16a regulates mitophagy. Cell (0092-8674) 2014 imex curation Soleimanpour S.A., Gupta A., Bakay M., Ferrari A.M., Groff D.N., Fadista J., Spruce L.A., Kushner J.A., Groop L., Seeholzer S.H., Kaufman B.A., Hakonarson H., Stoffers D.A. Diabetes - Interactions investigated in the context of Diabetes Microscopy and density gradient expts (Supp. Fig. 7) not included as they are with markers of subcellular location, not interacting proteins. stoffers@mail.med.upenn.edu 20-Oct-2014: Contacted by IntAct-Help. Only protein-protein interactions mouse-3t3 Mus musculus embryo cells 3t3 Mouse embryo fibroblast cells anti bait coip anti bait coimmunoprecipitation anti bait coip anti tag western anti tag western blot anti tag western Soleimanpour S.A., Gupta A., Bakay M., Ferrari A.M., Groff D.N., Fadista J., Spruce L.A., Kushner J.A., Groop L., Seeholzer S.H., Kaufman B.A., Hakonarson H., Stoffers D.A. Diabetes - Interactions investigated in the context of Diabetes Microscopy and density gradient expts (Supp. Fig. 7) not included as they are with markers of subcellular location, not interacting proteins. NIH 3T3 fibroblasts containing Flag-tagged Clec16a were grown in heavy isotopic abundance medium (13C6,15N2-lysine and 13C6,15N4-arginine), whereas wild-type cells were grown in light (12C, 14N), natural isotope abundance medium. Equal quantities of the two cell preparations were mixed, and the epitope-tagged protein complex was isolated. Specific protein interactions are identified by mass spectrometry as isotopically heavy, whereas non-specific interactions appear as a mixture of isotopically light and heavy. stoffers@mail.med.upenn.edu Accepted 2014-SEP-24 by MGT Cell (0092-8674) 2014 Only protein-protein interactions imex curation The diabetes susceptibility gene Clec16a regulates mitophagy. The diabetes susceptibility gene Clec16a regulates mitophagy. Cell (0092-8674) 2014 imex curation Soleimanpour S.A., Gupta A., Bakay M., Ferrari A.M., Groff D.N., Fadista J., Spruce L.A., Kushner J.A., Groop L., Seeholzer S.H., Kaufman B.A., Hakonarson H., Stoffers D.A. Diabetes - Interactions investigated in the context of Diabetes Microscopy and density gradient expts (Supp. Fig. 7) not included as they are with markers of subcellular location, not interacting proteins. stoffers@mail.med.upenn.edu 20-Oct-2014: Contacted by IntAct-Help. Only protein-protein interactions mouse-3t3 Mus musculus embryo cells 3t3 Mouse embryo fibroblast cells anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Soleimanpour S.A., Gupta A., Bakay M., Ferrari A.M., Groff D.N., Fadista J., Spruce L.A., Kushner J.A., Groop L., Seeholzer S.H., Kaufman B.A., Hakonarson H., Stoffers D.A. Diabetes - Interactions investigated in the context of Diabetes Microscopy and density gradient expts (Supp. Fig. 7) not included as they are with markers of subcellular location, not interacting proteins. NIH 3T3 fibroblasts containing Flag-tagged Clec16a were grown in heavy isotopic abundance medium (13C6,15N2-lysine and 13C6,15N4-arginine), whereas wild-type cells were grown in light (12C, 14N), natural isotope abundance medium. Equal quantities of the two cell preparations were mixed, and the epitope-tagged protein complex was isolated. Specific protein interactions are identified by mass spectrometry as isotopically heavy, whereas non-specific interactions appear as a mixture of isotopically light and heavy. stoffers@mail.med.upenn.edu Accepted 2014-SEP-24 by MGT Cell (0092-8674) 2014 Only protein-protein interactions imex curation The diabetes susceptibility gene Clec16a regulates mitophagy. The diabetes susceptibility gene Clec16a regulates mitophagy. Cell (0092-8674) 2014 imex curation Soleimanpour S.A., Gupta A., Bakay M., Ferrari A.M., Groff D.N., Fadista J., Spruce L.A., Kushner J.A., Groop L., Seeholzer S.H., Kaufman B.A., Hakonarson H., Stoffers D.A. Diabetes - Interactions investigated in the context of Diabetes Microscopy and density gradient expts (Supp. Fig. 7) not included as they are with markers of subcellular location, not interacting proteins. stoffers@mail.med.upenn.edu 20-Oct-2014: Contacted by IntAct-Help. Only protein-protein interactions mouse-3t3 Mus musculus embryo cells 3t3 Mouse embryo fibroblast cells anti tag coip anti tag coimmunoprecipitation anti tag coip sequence tag sequence tag identification sequence tag Soleimanpour S.A., Gupta A., Bakay M., Ferrari A.M., Groff D.N., Fadista J., Spruce L.A., Kushner J.A., Groop L., Seeholzer S.H., Kaufman B.A., Hakonarson H., Stoffers D.A. Diabetes - Interactions investigated in the context of Diabetes Microscopy and density gradient expts (Supp. Fig. 7) not included as they are with markers of subcellular location, not interacting proteins. NIH 3T3 fibroblasts containing Flag-tagged Clec16a were grown in heavy isotopic abundance medium (13C6,15N2-lysine and 13C6,15N4-arginine), whereas wild-type cells were grown in light (12C, 14N), natural isotope abundance medium. Equal quantities of the two cell preparations were mixed, and the epitope-tagged protein complex was isolated. Specific protein interactions are identified by mass spectrometry as isotopically heavy, whereas non-specific interactions appear as a mixture of isotopically light and heavy. stoffers@mail.med.upenn.edu Accepted 2014-SEP-24 by MGT Cell (0092-8674) 2014 Only protein-protein interactions imex curation rnf41_mouse E3 ubiquitin-protein ligase NRDP1 Rnf41 Flrf Nrdp1 RING finger protein 41 RING-type E3 ubiquitin transferase NRDP1 protein protein mouse Mus musculus Mouse MGYDVTRFQGDVDEDLICPICSGVLEEPVQAPHCEHAFCNACITQWFSQQQTCPVDRSVVTVAHLRPVPRIMRNMLSKLQIACDNAVFGCSAVVRLDNLMSHLSDCEHNPKRPVTCEQGCGLEMPKDELPNHNCIKHLRSVVQQQQSRIAELEKTSAEHKHQLAEQKRDIQLLKAYMRAIRSVNPNLQNLEETIEYNEILEWVNSLQPARVTRWGGMISTPDAVLQAVIKRSLVESGCPASIVNELIENAHERSWPQGLATLETRQMNRRYYENYVAKRIPGKQAVVVMACENQHMGDDMVQEPGLVMIFAHGVEEI mint 43FE844C06392802 q80u30-2 Protein CLEC16A Clec16a Kiaa0350 protein protein mouse Mus musculus Mouse MFGRSRSWVGGGHSKSSRNIHSLDHLKYLYHVLTKNTTVTEQNRNLLVETIRSITEILIWGDQNDSSVFDFFLEKNMFVFFLNILRQKSGRYVCVQLLQTLNILFENISHETSLYYLLSNNYVNSIIVHKFDFSDEEIMAYYISFLKTLSLKLNNHTVHFFYNEHTNDFALYTEAIKFFNHPESMVRIAVRTITLNVYKVDNQAMLHYIRDKTAVPYFSNLVWFIGSHVIELDNCVQTDEEHRNRGKLSDLVAEHLDHLHYLNDILIINCEFLNDVLTDHLLNRLFLPLYVYSLENPDKGGERPKISLPVSLYLLSQVFLIIHHAPLVNSLAEVILNGDLSETYTKPAQDVPRSSAKPSIRCFIKPTETLERSLEMNKHKGKKRMQKRPNYKNVGEEEDEERGSAEDAQEDAEKTKEIEMVIMKLGKLSEVAAAGTSVQEQNTTDEEKSAATNSENAQWSRPFLDMVYHALDSPDDDYHALFVLCLLYAMSHNKGMDPEKLKRIQLPVPSEAEKTTYNHLLAERLIRIMNNAAQPDGRIRLATLELSCLLLKQQVLTSSGCVIKDVHLACLEGAREESVHLVRHFYKGEEIFLDMFEDEYRSMTIKPMNVEYLMMDASILLPPTGTPLTGIDFVKRLPCGDVEKTRRAIRVFFMLRSLSLQLRGEPETQLPLTREEDLIKTDDVLDLNNSDLIACTVITKDGGMVQRFLAVDIYQMSLVEPDVSRLGWGVVKFAGLLQDMQVTGVEDDSRALNITIHKPASSPHSKPFPILQATFVFSDHIRCIIAKQRLAKGRIQARRMKMQRIAALLDLPIQPTTEVLGFGLCSSSSSSQHLPFRFYEQCRRGSSDPTVQRSVFASVDKVPGFAVAQCINQHSSPSLSSPSPPFASGSPGGSGSTSHCDSGGSSSAPSATQSPADAPTTPEQPQPHLDQSVIGNEMDVNSKPSKNSSARSSEGETMHLSPSLLPAQQPTISLLYEDTADTLSVESLTIVPPVDPHSLRALSGISQLPTLPAADTETPAEGAVNPEPAEPTEH BE47F3CA5AB7B4DA clec16a-rnf41 3 4 unspecified role unspecified role prey prey region identified peptide identified peptide certain certain sequence position certain certain certain sequence position certain region identified peptide identified peptide certain certain sequence position certain certain certain sequence position certain region identified peptide identified peptide certain certain sequence position certain certain certain sequence position certain region identified peptide identified peptide certain certain sequence position certain certain certain sequence position certain region identified peptide identified peptide certain certain sequence position certain certain certain sequence position certain region identified peptide identified peptide certain certain sequence position certain certain certain sequence position certain region identified peptide identified peptide certain certain sequence position certain certain certain sequence position certain region identified peptide identified peptide certain certain sequence position certain certain certain sequence position certain region identified peptide identified peptide certain certain sequence position certain certain certain sequence position certain region 13c label 13c label C13 13C C13 13C undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined region 15n label 15n label 15N N15 15N N15 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 5 unspecified role unspecified role bait bait c_terminus 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 region 13c label 13c label C13 13C C13 13C undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined region 15n label 15n label 15N N15 15N N15 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association Figs 1A-E clec16a-rnf41-2 2 4 unspecified role unspecified role prey prey 5 unspecified role unspecified role bait bait 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 physical association physical association Fig 1F rnf41-clec16a 1 4 unspecified role unspecified role bait bait 5 unspecified role unspecified role prey prey 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 physical association physical association Fig 1F