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/ SNX31: a novel sorting nexin associated with the uroplakin-degrading multivesicular bodies in terminally differentiated urothelial cells. SNX31: a novel sorting nexin associated with the uroplakin-degrading multivesicular bodies in terminally differentiated urothelial cells. PLoS ONE 2014 imex curation Vieira N., Deng F.M., Liang F.X., Liao Y., Chang J., Zhou G., Zheng W., Simon J.P., Ding M., Wu X.R., Romih R., Kreibich G., Sun T.T. Affinomics - Interactions curated for the Affinomics consortium. email sent 18/2 - species of Fig 8 -MDCK expt (dog) I have not annotated Fig 7 (sucrose density gradient) as this uses a "total" homogenate - and I dont think we do these... sunt01@nyumc.org Only protein-protein interactions imex curation mouse-urothelium mouse urothelium or uroepithelium uroepithelium Uroepithelium_or_urothelium confocal microscopy confocal microscopy immunocytochemistry immunocytochemistry Vieira N., Deng F.M., Liang F.X., Liao Y., Chang J., Zhou G., Zheng W., Simon J.P., Ding M., Wu X.R., Romih R., Kreibich G., Sun T.T. Affinomics - Interactions curated for the Affinomics consortium. Figure 1D: it is not stated that there is any co-loc shown here - but I can see some yellow areas on magnifying the image. (interaction is shown elsewhere) sunt01@nyumc.org Accepted 2015-MAR-16 by ORCHARD PLoS ONE 2014 imex curation SNX31: a novel sorting nexin associated with the uroplakin-degrading multivesicular bodies in terminally differentiated urothelial cells. SNX31: a novel sorting nexin associated with the uroplakin-degrading multivesicular bodies in terminally differentiated urothelial cells. PLoS ONE 2014 imex curation Vieira N., Deng F.M., Liang F.X., Liao Y., Chang J., Zhou G., Zheng W., Simon J.P., Ding M., Wu X.R., Romih R., Kreibich G., Sun T.T. Affinomics - Interactions curated for the Affinomics consortium. email sent 18/2 - species of Fig 8 -MDCK expt (dog) I have not annotated Fig 7 (sucrose density gradient) as this uses a "total" homogenate - and I dont think we do these... sunt01@nyumc.org Only protein-protein interactions imex curation in vitro In vitro filter binding filter binding Filter overlay assay Filter overlay assay anti tag western anti tag western blot anti tag western Vieira N., Deng F.M., Liang F.X., Liao Y., Chang J., Zhou G., Zheng W., Simon J.P., Ding M., Wu X.R., Romih R., Kreibich G., Sun T.T. Affinomics - Interactions curated for the Affinomics consortium. Results for the positive control -PIP2 -Grip-(N-terminal GST-tagged recombinant PLC-delta1 PH domain) have not been included as the origin of the construct is not known. sunt01@nyumc.org Accepted 2015-MAR-19 by ORCHARD PLoS ONE 2014 imex curation SNX31: a novel sorting nexin associated with the uroplakin-degrading multivesicular bodies in terminally differentiated urothelial cells. SNX31: a novel sorting nexin associated with the uroplakin-degrading multivesicular bodies in terminally differentiated urothelial cells. PLoS ONE 2014 imex curation Vieira N., Deng F.M., Liang F.X., Liao Y., Chang J., Zhou G., Zheng W., Simon J.P., Ding M., Wu X.R., Romih R., Kreibich G., Sun T.T. Affinomics - Interactions curated for the Affinomics consortium. email sent 18/2 - species of Fig 8 -MDCK expt (dog) I have not annotated Fig 7 (sucrose density gradient) as this uses a "total" homogenate - and I dont think we do these... sunt01@nyumc.org Only protein-protein interactions imex curation mouse-urothelium mouse urothelium or uroepithelium uroepithelium Uroepithelium_or_urothelium anti bait coip anti bait coimmunoprecipitation anti bait coip monoclonal western monoclonal antibody western blot monoclonal western Vieira N., Deng F.M., Liang F.X., Liao Y., Chang J., Zhou G., Zheng W., Simon J.P., Ding M., Wu X.R., Romih R., Kreibich G., Sun T.T. Affinomics - Interactions curated for the Affinomics consortium. email sent 18/2 - species of Fig 8 -MDCK expt (dog) I have not annotated Fig 7 (sucrose density gradient) as this uses a "total" homogenate - and I dont think we do these... sunt01@nyumc.org Accepted 2015-APR-01 by ORCHARD PLoS ONE 2014 Only protein-protein interactions imex curation imex curation MAL removed SNX31: a novel sorting nexin associated with the uroplakin-degrading multivesicular bodies in terminally differentiated urothelial cells. SNX31: a novel sorting nexin associated with the uroplakin-degrading multivesicular bodies in terminally differentiated urothelial cells. PLoS ONE 2014 imex curation Vieira N., Deng F.M., Liang F.X., Liao Y., Chang J., Zhou G., Zheng W., Simon J.P., Ding M., Wu X.R., Romih R., Kreibich G., Sun T.T. Affinomics - Interactions curated for the Affinomics consortium. email sent 18/2 - species of Fig 8 -MDCK expt (dog) I have not annotated Fig 7 (sucrose density gradient) as this uses a "total" homogenate - and I dont think we do these... sunt01@nyumc.org Only protein-protein interactions imex curation mouse-urothelium mouse urothelium or uroepithelium uroepithelium Uroepithelium_or_urothelium pla proximity ligation assay pELISA pELISA PLA antibody detection identification by antibody antibody detection Vieira N., Deng F.M., Liang F.X., Liao Y., Chang J., Zhou G., Zheng W., Simon J.P., Ding M., Wu X.R., Romih R., Kreibich G., Sun T.T. Affinomics - Interactions curated for the Affinomics consortium. sunt01@nyumc.org Accepted 2015-MAR-16 by ORCHARD PLoS ONE 2014 imex curation SNX31: a novel sorting nexin associated with the uroplakin-degrading multivesicular bodies in terminally differentiated urothelial cells. SNX31: a novel sorting nexin associated with the uroplakin-degrading multivesicular bodies in terminally differentiated urothelial cells. PLoS ONE 2014 imex curation Vieira N., Deng F.M., Liang F.X., Liao Y., Chang J., Zhou G., Zheng W., Simon J.P., Ding M., Wu X.R., Romih R., Kreibich G., Sun T.T. Affinomics - Interactions curated for the Affinomics consortium. email sent 18/2 - species of Fig 8 -MDCK expt (dog) I have not annotated Fig 7 (sucrose density gradient) as this uses a "total" homogenate - and I dont think we do these... sunt01@nyumc.org Only protein-protein interactions imex curation mouse-urothelium mouse urothelium or uroepithelium uroepithelium Uroepithelium_or_urothelium tem transmission electron microscopy tem immunocytochemistry immunocytochemistry Vieira N., Deng F.M., Liang F.X., Liao Y., Chang J., Zhou G., Zheng W., Simon J.P., Ding M., Wu X.R., Romih R., Kreibich G., Sun T.T. Affinomics - Interactions curated for the Affinomics consortium. I dont see what they have done for the gold staining - the reference makes little sense, and it would not be possible to use Protein A as stated in the methods section here, as Protein A would bind to both antibodies?? So I have omitted any mention of gold in the exp-mod. Umbrella cells;flattened extendible cells forming the outermost layer. sunt01@nyumc.org Accepted 2015-MAR-16 by ORCHARD PLoS ONE 2014 imex curation upk3a_mouse Uroplakin-3a Upk3a Upk3 Uroplakin III protein protein mouse Mus musculus Mouse MLLLWALLALGCLRCGWTVNLQPQLASVTFATNNPTLTTVALEKPLCMFDSSEPLSGSYEVYLYAMVDSAMSRNVSVQDSAGVPLSTTFRQTQGGRSGPYKAAAFDLTPCGDLPSLDAVGDVTQASEILNAYLVRVGNNGTCFWDPNFQGLCNPPLTAATEYRFKYVLVNMSTGLVQDQTLWSDPIWTNRPIPYSAIDTWPGRRSGGMIVITSILGSLPFFLLVGFAGAIILSFVDMGSSDGEMTHDSQITQEAVPKTLGTSEPSYSSVNRGPPLDRAEVFSSKLQD mint Component of the asymmetric unit membrane (AUM); a highly specialized biomembrane elaborated by terminally differentiated urothelial cells. May play an important role in AUM-cytoskeleton interaction in terminally differentiated urothelial cells. It also contributes to the formation of urothelial glycocalyx which may play an important role in preventing bacterial adherence 44CF39DA6CA30E88 snx31_mouse Sorting nexin-31 Snx31 protein protein mouse Mus musculus Mouse MKMHFCIPVSQQRPDALGGRYVLYSVYLDGFLFCKVRYSQLHRWDEQLRRVFGNCLPPFPPKYYLAMTTAMAEERRDQLERYLQNVTADPRVTRSDVFTEFLTLVQLHTLNITIQNVELAVFLPDGRSIKVEGLTSDTAERVLEVMAHKLGLQPDLVGYFGLFLIQCFPEGKLSVVKKLADFELPYTSLQSSEMENCKIGLRKWYLDPALDSMLMDCRAAGDLLYMQAVQDIEKEWMKPTQAQREELKALQKKENQTKFLELSQEVRHYGYVQLDPCTCNHPEPGCGAQLSIGNNEISCCITLPNGQIQDIAFQMSRVKCWQVTFLGTLLDTDGPQRTLNQNLELRFQYSEDSCQQWFVIYTKQAFFLSSCLKKMISERMTKLTEQSPEMQIEVPEQGRSKKHPSQPSQQKVYFNFLRKGKMKRSEGDYVWDTLMEEGL 7EBA127EF76BE397 phosphatidylinositol-3-phosphate phosphatidylinositol 3-phosphate phosphatidylinositol 3-phosphates PI(3)P PtdIns3P small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) upk1b_mouse Uroplakin-1b Upk1b Uroplakin Ib protein protein mouse Mus musculus Mouse MAKDDSTVRCFQGLLIFGHVIVGMCGIALTAECIFFVSDQHSLYPLLEATNNDDIFGAAWIGMFVGICLFCLSVLAIVGIMKSNRKILLAYFIMMFIVYGFEVASCITAATQRDFFTTNLFLKQMLMRYQNNSPPTNDDEWKNNGVTKTWDRLMLQDHCCGVNGPSDWQKYTSAFRVENNDADYPWPRQCCVMDKLKEPLNLDACKLGVPGYYHSQGCYELISGPMDRHAWGVAWFGFAILCWTFWVLLGTMFYWSRIEY 91EB5816D59070A4 snx31-upk3a-4 1 6 unspecified role unspecified role neutral component neutral component 7 unspecified role unspecified role neutral component neutral component colocalization colocalization 1D, 6 D/F,9 Mice with the Buff -Vps33a D251E mutation show an augmented interaction. UPII-knockout snx31-upk3a-1 5 6 unspecified role unspecified role neutral component neutral component 7 unspecified role unspecified role neutral component neutral component colocalization colocalization 3G Co-localization is seen at the limiting membranes of multivesicular bodies snx31-mal-1 3 6 unspecified role unspecified role prey prey 9 unspecified role unspecified role prey prey 7 unspecified role unspecified role bait bait association association 6A (B) snx31-upk3a-2 1 6 unspecified role unspecified role neutral component neutral component 9 unspecified role unspecified role neutral component neutral component colocalization colocalization 6C/E positive control snx31-upk3a-5 4 6 unspecified role unspecified role neutral component neutral component 9 unspecified role unspecified role neutral component neutral component proximity proximity close-contact colocalization neighbourhood interaction 6 G/I positive control snx31-upk3a-3 4 6 unspecified role unspecified role neutral component neutral component 7 unspecified role unspecified role neutral component neutral component proximity proximity close-contact colocalization neighbourhood interaction 6 H/J Mice with the Buff -Vps33a D251E mutation show an augmented interaction. phosphatidylinositol_trisphosphate-snx31-1 2 8 unspecified role unspecified role bait bait chemical synthesis Chemical synthesis (Chemical synthesis) 7 unspecified role unspecified role prey prey c_terminus 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 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. physical association physical association 10