8B8I | pdb_00008b8i

Nanobody (NbLumSyt1) bound to human Syt1

PDB DOI: https://doi.org/10.2210/pdb8B8I/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Vicugna pacos, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-10-04 Released: 2024-04-17
Deposition Author(s): Liu, H., Scaletti, E., Stenmark, P.
Funding Organization(s): Swedish Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.298 (Depositor), 0.303 (DCC)
R-Value Work:
0.263 (Depositor), 0.283 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

A versatile nanobody platform for live and super-resolution imaging of synaptic vesicle dynamics and plasticity in rodent and human neurons.

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.

(2026) J Nanobiotechnology 24

PubMed: 42135832 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1186/s12951-026-04489-w
Primary Citation Related Structures:
8B8I

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.

Organizational Affiliation

Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany.

Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany.

Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany.

Bioanalytical Mass Spectrometry Research Group, Max Planck Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany.

Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany.

Clinic of Neurology, University Medical Center Göttingen, 37075, Göttingen, Germany.

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125, Berlin, Germany.

NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, 10117, Berlin, Germany.

Department of Applied Physics and SciLifeLab, KTH Royal Institute of Technology, Stockholm, 17165, Sweden.

8 VIB-KU Leuven Center for Neuroscience, Leuven, 3000, Belgium.

Department of Neurosciences, Leuven Brain Institute, Belgium and KU Leuven, Leuven, 3000, Belgium.

Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Wuerzburg, 97080, Wuerzburg, Germany.

Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.

Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-106 91, Sweden.

Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, 37075, Göttingen, Germany.

Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, Scotland, UK.

Simons Initiative for the Developing Brain, University of Edinburgh, Hugh Robson Building, Edinburgh, EH8 9XD, Scotland, UK.

Muir Maxwell Epilepsy Centre, University of Edinburgh, Hugh Robson Building, Edinburgh, EH8 9XD, Scotland, UK.

Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.

Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia.

School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.

Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN, 37240-7933, USA.

Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, 37240-7933, USA.

Faculty of Biology, Freie Universität Berlin, 14195, Chemistry, Pharmacy, Berlin, Germany.

Fraunhofer Institute for Translational Medicine and Pharmacology ITMP,, Translational Neuroinflammation and Automated Microscopy, 37075, Göttingen, Germany.

Bioanalytics, Department of Clinical Chemistry, University Medical Center Göttingen, 37075, Göttingen, Germany.

Cluster of Excellence ″Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells″ (MBExC), University of Göttingen, 37075, Göttingen, Germany.

NanoTag Biotechnologies GmbH, 37079, Göttingen, Germany.

Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany. efornas@gwdg.de.

Department of Life Sciences, University of Trieste, Trieste, 34127, Italy. efornas@gwdg.de.

Macromolecule Content

Total Structure Weight: 152.48 kDa
Atom Count: 7,778
Modeled Residue Count: 1,052
Deposited Residue Count: 1,424
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody (NbLumSyt1)	A, B, C, D, E A, B, C, D, E, F, G, H	118	Vicugna pacos	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptotagmin-1	I, J, K, L, M I, J, K, L, M, N, O, P	60	Homo sapiens	Mutation(s): 0 Gene Names: SYT1, SVP65, SYT
UniProt & NIH Common Fund Data Resources
Find proteins for P21579 (Homo sapiens) Explore P21579 Go to UniProtKB: P21579
PHAROS: P21579 GTEx: ENSG00000067715
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21579
Sequence Annotations Expand
Reference Sequence