8B8I

Nanobody (NbLumSyt1) bound to human Syt1

Summary for 8B8I

• Entry DOI: 10.2210/pdb8b8i/pdb
• Descriptor: Nanobody (NbLumSyt1), Synaptotagmin-1 (3 entities in total)
• Functional Keywords: syt1, nanobody, peptide binding protein
• Biological source: Vicugna pacos; More
• Total number of polymer chains: 16
• Total formula weight: 152482.12

Authors

Liu, H.,Scaletti, E.,Stenmark, P. (deposition date: 2022-10-04, release date: 2024-04-17, Last modification date: 2026-06-10)

Primary citation

Goel, R.,Jevdokimenko, K.,Rehm, R.,Hentze, J.,Agui-Gonzalez, P.,Ninov, M.,Maier, E.,Wu, Y.,Lange, F.,Witkowska, A.,Bolz, S.,Pennacchietti, F.,Damenti, M.,Kaempf, N.,Khayenko, V.,Calatayud, C.,Malviya, V.N.,Chanaday, N.L.,Hutchinson, E.S.,Liu, H.,Weyand, K.,Schwarze, V.,Ivanova, D.,Wallis, T.P.,Small, C.,Maric, H.M.,Joensuu, M.,Cousin, M.A.,Meunier, F.A.,Verstreken, P.,Testa, I.,Kavalali, E.T.,Haucke, V.,Jakobs, S.,Urlaub, H.,Brose, N.,Cooper, B.H.,Stenmark, P.,Opazo, F.,Jahn, R.,Rizzoli, S.O.,Fornasiero, E.F.
A versatile nanobody platform for live and super-resolution imaging of synaptic vesicle dynamics and plasticity in rodent and human neurons.
J Nanobiotechnology, 24:-, 2026

PubMed Abstract: Synaptic neurotransmission is a critical hallmark of brain activity and one of the first processes affected in neural diseases. Monitoring this process, particularly synaptic vesicle recycling, in living cells has been instrumental in revealing the mechanisms responsible for neurotransmitter release. However, currently available reporters suffer from limitations, such as large probe sizes or limited compatibility for human neurons, hampering the quantitative analysis of synaptic pathophysiology. Here, we describe the NbLumSyt1 toolkit, a panel of nanobody-based affinity probes that target the luminal domain of the synaptic vesicle protein Synaptotagmin 1 (Syt1). These new tools enable quantitative, noninvasive imaging and functional interrogation of Syt1 exo-endocytosis and trafficking in human neurons, with unprecedented precision, versatility and cost efficiency, in technologies ranging from fixed- and live-cell super-resolution imaging to electron microscopy and mass spectrometry. Overall, NbLumSyt1 nanobinders provide a valuable platform for studying synaptic physiology and pathophysiology, benefiting fundamental neuroscience and translational efforts to study and develop treatments for brain-related disorders.

PubMed: 42135832
DOI: 10.1186/s12951-026-04489-w

Experimental method

X-RAY DIFFRACTION (2.75 Å)