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Modified composition of \u03b3-secretase or mutations in its subunits has been directly linked to altered generation of Amyloid beta. Despite biochemical evidence about the role of \u03b3-secretase in the generation of APP, the molecular origin of how spatial heterogeneity in the generation of proteoforms arises is not well understood. Here, we evaluated the localization of Nicastrin, a \u03b3-secretase subunit, at nanometer sized functional zones of the synapse. With the help of super resolution microscopy, we confirm that Nicastrin is organized into nanodomains of high molecular density within an excitatory synapse. A similar nanoorganization was also observed for APP and the catalytic subunit of \u03b3-secretase, Presenilin 1, that were discretely associated with Nicastrin nanodomains. Though Nicastrin is a functional subunit of \u03b3-secretase, the Nicastrin and Presenilin1 nanodomains were either colocalized or localized independent of each other. The Nicastrin and Presenilin domains highlight a potential independent regulation of these molecules different from their canonical secretase function. The collisions between secretases and substrate molecules decide the probability and rate of product formation for transmembrane proteolysis. Our observations of secretase nanodomains indicate a spatial difference in the confinement of substrate and secretases, affecting the local probability of product formation by increasing their molecular availability, resulting in differential generation of proteoforms even within single synapses.<\/jats:p>","DOI":"10.1186\/s13041-021-00855-x","type":"journal-article","created":{"date-parts":[[2021,10,13]],"date-time":"2021-10-13T13:17:30Z","timestamp":1634131050000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Nanoscale organization of Nicastrin, the substrate receptor of the \u03b3-secretase complex, as independent molecular domains"],"prefix":"10.1186","volume":"14","author":[{"given":"Shekhar","family":"Kedia","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kousik","family":"Mandal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pallavi Rao","family":"Netrakanti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mini","family":"Jose","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sangram S.","family":"Sisodia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2103-1653","authenticated-orcid":false,"given":"Deepak","family":"Nair","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,10,13]]},"reference":[{"key":"855_CR1","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/S0896-6273(03)00205-8","volume":"38","author":"B De Strooper","year":"2003","unstructured":"De Strooper B. Aph-1, Pen-2, and Nicastrin with Presenilin generate an active \u03b3-Secretase complex. Neuron. 2003;38:9\u201312.","journal-title":"Neuron"},{"key":"855_CR2","first-page":"342","volume":"7","author":"N Gertsik","year":"2015","unstructured":"Gertsik N, Chiu D, Li YM. Complex regulation of \u03b3-secretase: from obligatory to modulatory subunits. Front Aging Neurosci. 2015;7:342.","journal-title":"Front Aging Neurosci"},{"key":"855_CR3","doi-asserted-by":"publisher","first-page":"3272","DOI":"10.1523\/JNEUROSCI.23-08-03272.2003","volume":"23","author":"T Li","year":"2003","unstructured":"Li T, Ma G, Cai H, Price DL, Wong PC. Nicastrin is required for assembly of presenilin\/\u03b3-secretase complexes to mediate notch signaling and for processing and trafficking of \u03b2-amyloid precursor protein in mammals. 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