Synaptotagmin-1 and neuronal SNARE proteins have central roles in evoked synchronous neurotransmitter release; however, it is unknown how they cooperate to trigger synaptic vesicle fusion. Here we report atomic-resolution crystal structures of Ca2+- and Mg2+-bound complexes between synaptotagmin-1 and the neuronal SNARE complex, one of which was determined with diffraction data from an X-ray free-electron laser, leading to an atomic-resolution structure with accurate rotamer assignments for many side chains. The structures reveal several interfaces, including a large, specific, Ca2+-independent and conserved interface. Tests of this interface by mutagenesis suggest that it is essential for Ca2+-triggered neurotransmitter release in mouse hippocampal neuronal synapses and for Ca2+-triggered vesicle fusion in a reconstituted system. We propose that this interface forms before Ca2+ triggering, moves en bloc as Ca2+ influx promotes the interactions between synaptotagmin-1 and the plasma membrane, and consequently remodels the membrane to promote fusion, possibly in conjunction with other interfaces.
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Wickner, W. & Schekman, R. Membrane fusion. Nature Struct. Mol. Biol. 15, 658–664 (2008)
Rothman, J. E. The Principle of Membrane Fusion in the Cell (Nobel Lecture). Angew. Chemie Int. Ed. 53, 12676–12694 (2014)
Sutton, R. B., Fasshauer, D., Jahn, R. & Brunger, A. T. Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 Å resolution. Nature 395, 347–353 (1998)
Weber, T. et al. SNAREpins: minimal machinery for membrane fusion. Cell 92, 759–772 (1998)
Südhof, T. C. Neurotransmitter release: the last millisecond in the life of a synaptic vesicle. Neuron 80, 675–690 (2013)
Pang, Z. P. & Südhof, T. C. Cell biology of Ca2+-triggered exocytosis. Curr. Opin. Cell Biol. 22, 496–505 (2010)
Geppert, M. et al. Synaptotagmin I: a major Ca2+ sensor for transmitter release at a central synapse. Cell 79, 717–727 (1994)
Xu, J., Mashimo, T. & Südhof, T. C. Synaptotagmin-1, -2, and -9: Ca2+ sensors for fast release that specify distinct presynaptic properties in subsets of neurons. Neuron 54, 567–581 (2007)
Wen, H. et al. Distinct roles for two synaptotagmin isoforms in synchronous and asynchronous transmitter release at zebrafish neuromuscular junction. Proc. Natl Acad. Sci. USA 107, 13906–13911 (2010)
Bacaj, T. et al. Synaptotagmin-1 and synaptotagmin-7 trigger synchronous and asynchronous phases of neurotransmitter release. Neuron 80, 947–959 (2013)
Yoshihara, M. & Littleton, J. T. Synaptotagmin I functions as a calcium sensor to synchronize neurotransmitter release. Neuron 36, 897–908 (2002)
Maximov, A. & Südhof, T. C. Autonomous function of synaptotagmin 1 in triggering synchronous release independent of asynchronous release. Neuron 48, 547–554 (2005)
Kochubey, O. & Schneggenburger, R. Synaptotagmin increases the dynamic range of synapses by driving Ca2+-evoked release and by clamping a near-linear remaining Ca2+ sensor. Neuron 69, 736–748 (2011)
Davletov, B. A. & Südhof, T. C. A single C2 domain from synaptotagmin I is sufficient for high affinity Ca2+/phospholipid binding. J. Biol. Chem. 268, 26386–26390 (1993)
Brose, N., Petrenko, A. G., Südhof, T. C. & Jahn, R. Synaptotagmin: a calcium sensor on the synaptic vesicle surface. Science 256, 1021–1025 (1992)
Fernández-Chacón, R. et al. Synaptotagmin I functions as a calcium regulator of release probability. Nature 410, 41–49 (2001)
Vrljic, M. et al. Post-translational modifications and lipid binding profile of insect cell-expressed full-length mammalian synaptotagmin 1. Biochemistry 50, 9998–10012 (2011)
Rhee, J.-S. et al. Augmenting neurotransmitter release by enhancing the apparent Ca2+ affinity of synaptotagmin 1. Proc. Natl Acad. Sci. USA 102, 18664–18669 (2005)
Araç, D. et al. Close membrane-membrane proximity induced by Ca2+-dependent multivalent binding of synaptotagmin-1 to phospholipids. Nature Struct. Mol. Biol. 13, 209–217 (2006)
Hui, E., Johnson, C. P., Yao, J., Dunning, F. M. & Chapman, E. R. Synaptotagmin-mediated bending of the target membrane is a critical step in Ca2+-regulated fusion. Cell 138, 709–721 (2009)
Martens, S., Kozlov, M. M. & McMahon, H. T. How synaptotagmin promotes membrane fusion. Science 316, 1205–1208 (2007)
Zhang, X., Rizo, J. & Südhof, T. C. Mechanism of phospholipid binding by the C2A-domain of synaptotagmin I. Biochemistry 37, 12395–12403 (1998)
Rufener, E., Frazier, A. A., Wieser, C. M., Hinderliter, A. & Cafiso, D. S. Membrane-bound orientation and position of the synaptotagmin C2B domain determined by site-directed spin labeling. Biochemistry 44, 18–28 (2005)
Bennett, M. K., Calakos, N. & Scheller, R. H. Syntaxin: a synaptic protein implicated in docking of synaptic vesicles at presynaptic active zones. Science 257, 255–259 (1992)
Li, C. et al. Ca2+-dependent and -independent activities of neural and non-neural synaptotagmins. Nature 375, 594–599 (1995)
Pang, Z. P., Shin, O.-H., Meyer, A. C., Rosenmund, C. & Südhof, T. C. A gain-of-function mutation in synaptotagmin-1 reveals a critical role of Ca2+-dependent soluble N-ethylmaleimide-sensitive factor attachment protein receptor complex binding in synaptic exocytosis. J. Neurosci. 26, 12556–12565 (2006)
Rickman, C. et al. Conserved prefusion protein assembly in regulated exocytosis. Mol. Biol. Cell 17, 283–294 (2006)
Choi, U. B. et al. Single-molecule FRET-derived model of the synaptotagmin 1-SNARE fusion complex. Nature Struct. Mol. Biol. 17, 318–324 (2010)
Dai, H., Shen, N., Araç, D. & Rizo, J. A quaternary SNARE-synaptotagmin-Ca2+-phospholipid complex in neurotransmitter release. J. Mol. Biol. 367, 848–863 (2007)
Brewer, K. D. et al. Dynamic binding mode of a Synaptotagmin-1–SNARE complex in solution. Nature Struct. Mol. Biol. 22, 555–564 (2015)
Sutton, R. B., Davletov, B. A., Berghuis, A. M., Südhof, T. C. & Sprang, S. R. Structure of the first C2 domain of synaptotagmin I: a novel Ca2+/phospholipid-binding fold. Cell 80, 929–938 (1995)
Fernandez, I. et al. Three-dimensional structure of the synaptotagmin 1 C2B-domain: synaptotagmin 1 as a phospholipid binding machine. Neuron 32, 1057–1069 (2001)
Fuson, K. L., Montes, M., Robert, J. J. & Sutton, R. B. Structure of human synaptotagmin 1 C2AB in the absence of Ca2+ reveals a novel domain association. Biochemistry 46, 13041–13048 (2007)
Redecke, L. et al. Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser. Science 339, 227–230 (2013)
Gaffaney, J. D., Dunning, F. M., Wang, Z., Hui, E. & Chapman, E. R. Synaptotagmin C2B domain regulates Ca2+-triggered fusion in vitro: critical residues revealed by scanning alanine mutagenesis. J. Biol. Chem. 283, 31763–31775 (2008)
Xue, M., Ma, C., Craig, T. K., Rosenmund, C. & Rizo, J. The Janus-faced nature of the C2B domain is fundamental for synaptotagmin-1 function. Nature Struct. Mol. Biol. 15, 1160–1168 (2008)
Diao, J. et al. Synaptic proteins promote calcium-triggered fast transition from point contact to full fusion. Elife 1, e00109 (2012)
Lai, Y. et al. Complexin inhibits spontaneous release and synchronizes Ca2+-triggered synaptic vesicle fusion by distinct mechanisms. Elife 3, 1–14 (2014)
Suh, B.-C. & Hille, B. Electrostatic interaction of internal Mg2+ with membrane PIP2 Seen with KCNQ K+ channels. J. Gen. Physiol. 130, 241–256 (2007)
Park, Y. et al. Controlling synaptotagmin activity by electrostatic screening. Nature Struct. Mol. Biol. 19, 991–997 (2012)
Xu, J., Pang, Z. P., Shin, O.-H. & Südhof, T. C. Synaptotagmin-1 functions as a Ca2+ sensor for spontaneous release. Nature Neurosci. 12, 759–766 (2009)
Krishnakumar, S. S. et al. Conformational dynamics of calcium-triggered activation of fusion by synaptotagmin. Biophys. J. 105, 2507–2516 (2013)
Wang, J. et al. Calcium sensitive ring-like oligomers formed by synaptotagmin. Proc. Natl Acad. Sci. USA 111, 13966–13971 (2014)
Masumoto, T. et al. Ca2+-independent syntaxin binding to the C2B effector region of synaptotagmin. Mol. Cell. Neurosci. 49, 1–8 (2012)
Mackler, J. & Reist, N. Mutations in the second C2 domain of synaptotagmin disrupt synaptic transmission at Drosophila neuromuscular junctions. J. Comp. Neurol. 436, 4–16 (2001)
Gao, Y. et al. Single reconstituted neuronal SNARE complexes zipper in three distinct stages. Science 337, 1340–1343 (2012)
Zhou, P., Bacaj, T., Yang, X., Pang, Z. P. & Südhof, T. C. Lipid-anchored SNAREs lacking transmembrane regions fully support membrane fusion during neurotransmitter release. Neuron 80, 470–483 (2013)
Aeffner, S., Reusch, T., Weinhausen, B. & Salditt, T. Energetics of stalk intermediates in membrane fusion are controlled by lipid composition. Proc. Natl Acad. Sci. USA 109, E1609–E1618 (2012)
Chen, X. et al. Three-dimensional structure of the complexin/SNARE complex. Neuron 33, 397–409 (2002)
Tang, J. et al. A complexin/synaptotagmin 1 switch controls fast synaptic vesicle exocytosis. Cell 126, 1175–1187 (2006)
van Leeuwen, H. C., Strating, M. J., Rensen, M., De Laat, W. & Van Der Vliet, P. C. Linker length and composition influence the flexibility of Oct-1 DNA binding. EMBO J. 16, 2043–2053 (1997)
Ismail, S. A., Vetter, I. R., Sot, B. & Wittinghofer, A. The structure of an Arf-ArfGAP complex reveals a Ca2+ regulatory mechanism. Cell 141, 812–821 (2010)
Ernst, J. A. & Brunger, A. T. High resolution structure, stability, and synaptotagmin binding of a truncated neuronal SNARE complex. J. Biol. Chem. 278, 8630–8636 (2003)
Cipriano, D. J. et al. Processive ATP-driven disassembly of SNARE complexes by the N-ethylmaleimide sensitive factor molecular machine. J. Biol. Chem. (2013)
Studier, F. W. Protein production by auto-induction in high-density shaking cultures. Protein Expr. Purif. 41, 207–234 (2005)
Bonifacio, R., Pellegrini, C. & Narducci, L. M. Collective instabilities and high-gain regime in a free electron laser. Opt. Commun. 50, 373–378 (1984)
Kondratenko, A. M. & Saldin, E. L. Generation of coherent radiation by a relativistic electron beam in an undulator. Part. Accel. 10, 207–216 (1980)
Neutze, R., Wouts, R., van der Spoel, D., Weckert, E. & Hajdu, J. Potential for biomolecular imaging with femtosecond X-ray pulses. Nature 406, 752–757 (2000)
Solem, J. C. Imaging biological specimens with high-intensity soft x rays. J. Opt. Soc. Am. B 3, 1551 (1986)
Cohen, A. E. et al. Goniometer-based femtosecond crystallography with X-ray free electron lasers. Proc. Natl Acad. Sci. USA 111, 17122–17127 (2014)
Zeldin, O. B. et al. Data exploration toolkit for serial diffraction experiments. Acta Crystallogr. D 71, 352–356 (2015)
Hattne, J. et al. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers. Nature Methods 11, 545–548 (2014)
Sauter, N. K., Hattne, J., Grosse-Kunstleve, R. W. & Echols, N. New Python-based methods for data processing. Acta Crystallogr. D 69, 1274–1282 (2013)
Sauter, N. K. et al. Improved crystal orientation and physical properties from single-shot XFEL stills. Acta Crystallogr. D 70, 3299–3309 (2014)
Uervirojnangkoorn, M. et al. Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals. Elife 4, e05421 (2015)
Kabsch, W. XDS. Acta Crystallogr. D 66, 125–132 (2010)
Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D 67, 235–242 (2011)
McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007)
Emsley, P. & Cowtan, K. Coot: Model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)
Brunger, A. T. Version 1.2 of the Crystallography and NMR system. Nature Protocols 2, 2728–2733 (2007)
Brunger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)
Adams, P. D. et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D 58, 1948–1954 (2002)
Schröder, G. F., Levitt, M. & Brunger, A. T. Super-resolution biomolecular crystallography with low-resolution data. Nature 464, 1218–1222 (2010)
Urzhumtseva, L., Afonine, P. V., Adams, P. D. & Urzhumtsev, A. Crystallographic model quality at a glance. Acta Crystallogr. D 65, 297–300 (2009)
Chen, V. B. et al. MolProbity: All-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010)
Pettersen, E. F. et al. UCSF Chimera - A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004)
Krissinel, E. & Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774–797 (2007)
Young, S. M. & Neher, E. Synaptotagmin has an essential function in synaptic vesicle positioning for synchronous release in addition to its role as a calcium sensor. Neuron 63, 482–496 (2009)
de Wit, H. et al. Synaptotagmin-1 docks secretory vesicles to syntaxin-1/SNAP-25 acceptor complexes. Cell 138, 935–946 (2009)
Mohrmann, R. et al. Synaptotagmin interaction with SNAP-25 governs vesicle docking, priming, and fusion triggering. J. Neurosci. 33, 14417–14430 (2013)
Kyoung, M. et al. In vitro system capable of differentiating fast Ca2+-triggered content mixing from lipid exchange for mechanistic studies of neurotransmitter release. Proc. Natl Acad. Sci. USA 108, E304–E313 (2011)
Kyoung, M., Zhang, Y., Diao, J., Chu, S. & Brunger, A. T. Studying calcium-triggered vesicle fusion in a single vesicle-vesicle content and lipid-mixing system. Nature Protocols 8, 1–16 (2013)
Lee, H.-K. et al. Dynamic Ca2+-dependent stimulation of vesicle fusion by membrane-anchored synaptotagmin 1. Science 328, 760–763 (2010)
Lai, Y., Lou, X., Jho, Y., Yoon, T.-Y. & Shin, Y.-K. The synaptotagmin 1 linker may function as an electrostatic zipper that opens for docking but closes for fusion pore opening. Biochem. J. 456, 25–33 (2013)
Wang, Z., Liu, H., Gu, Y. & Chapman, E. R. Reconstituted synaptotagmin I mediates vesicle docking, priming, and fusion. J. Cell Biol. 195, 1159–1170 (2011)
Zick, M. & Wickner, W. T. A distinct tethering step is vital for vacuole membrane fusion. Elife 3, e03251 (2014)
Maximov, A., Pang, Z. P., Tervo, D. G. R. & Südhof, T. C. Monitoring synaptic transmission in primary neuronal cultures using local extracellular stimulation. J. Neurosci. Methods 161, 75–87 (2007)
We thank M. S. Padolina for help with protein purification, the Northeastern Collaborative Access Team (supported by NIH P41 GM103403) at Advanced Photon Source for X-ray data collection, and the SSRL/LCLS scientists E. L. Baxter, P. Ehrensberger, T. I. Eriksson, Y. Feng, M. Hollenbeck, E. G. Kovaleva, S. E. McPhillips, S. Nelson, J. Song, Y. Tsai, V. Vinetsky and D. Zhu for their invaluable assistance with data collection at the LCLS XPP facility. Use of the Stanford Synchrotron Radiation Lightsource (SSRL) and Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, is supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences under contract no. DE-AC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research, and by the National Institutes of Health, National Institute of General Medical Sciences (including P41GM103393). Portions of this research were carried out at the Linac Coherent Light Source (LCLS) at the SLAC National Accelerator Laboratory. LCLS is an Office of Science User Facility operated for the US Department of Energy Office of Science by Stanford University. This research was supported in part by the National Institutes of Health (R37MH63105 to A.T.B.; MH086403 to T.C.S.; GM095887 and GM102520 to N.K.S and A.S.B); and by a HHMI Collaborative Innovation Award (HCIA) to A.T.B. and W.I.W.
The authors declare no competing financial interests.
Extended data figures and tables
a, Diagram of the Duet co-expression vectors (Novagen) that express the fragments of the neuronal SNARE complex and the C2AB-linker-SNAP-25_C chimaera used for purification and crystallization of the Syt1–SNARE37aa-linker complex. The rat syntaxin-1A and His-tagged rat synaptobrevin-2 fragments were cloned into the vector pACYCDuet-1; the C2AB-linker-SNAP-25_C chimaera and the SNAP-25_N fragment were cloned into the vector pETDuet-1 with amino acid ranges labelled. Dashed lines represent the 37-amino-acid linker (see Methods). b, The purified Syt1–SNARE37aa-linker complex eluted as a single peak during size-exclusion chromatography (profile on the left). Left gel: Coomassie-blue-stained SDS–PAGE gel of the purified Syt1–SNARE37aa-linker complex (unboiled and boiled). Right gel: Coomassie-blue-stained SDS–PAGE gel of dissolved crystals of the Syt1–SNARE complex that were grown over a period of 2 months starting from purified Syt1–SNARE37aa-linker (unboiled and boiled). Although Syt1 was initially covalently linked to SNAP-25_C, the linker was cleaved during crystallization. The comparison between boiled and unboiled lanes is a hallmark showing that neuronal SNARE complex is fully formed. c, Boiled Coomassie-blue-stained SDS–PAGE gel of the purified Syt1–SNARE37aa-linker complex in solution at ambient temperature at the specified time after purification. Cleavage is apparent on day one and progresses slowly over several days. d, Schema showing the commonly used vapour-diffusion technique: the drop contains a lower concentration of the precipitant than the reservoir. The crystallization of the quintuple mutant of Syt1 C2B is used as an example. e, Schema showing a reverse vapour-diffusion method that was used for crystallization of the Ca2+-bound Syt1–SNARE complex: the drop contains a higher concentration of the precipitant than the reservoir.
Extended Data Figure 2 Diffraction images, electron density maps and crystal packing of the Syt1–SNARE complex in the long unit cell crystal form.
a, Only one out of 85 screened crystals in the long unit cell crystal form diffracted to 4.1 Å resolution at the APS NE-CAT microfocus synchrotron beamline (a total of 105 crystals were screened with 20 that indexed in the short unit cell crystal form). b, A total of 61 out of ∼72 crystals in the long unit cell crystal form diffracted to at least 3.5 Å resolution at the LCLS XFEL (a total of 148 crystals were diffracted, out of those 113 crystals produced 578 images that could be processed; 35 crystals did not diffract or showed multiple lattices). These exposures were taken along the crystal c axis. The left upper pictures in a and b show images of loop-mounted crystals after X-ray exposure. c, mFo − DFc annealed omit map (Methods) of the Ca2+-bound Syt1–SNARE complex in the long unit cell crystal form using diffraction data collected at the LCLS XFEL; omitted residues within region I of the primary interface (residues 335–340 in Syt1 and 159–166 in SNAP-25) are coloured cyan. The contour level is 2.3σ. d–f, Representative 2mFo − DFc electron density maps of the Ca2+-bound Syt1–SNARE complex in the long unit cell crystal form using diffraction data collected at the LCLS XFEL. The contour level is 1.5σ. g, Views of the crystal lattice perpendicular to the bc (left) and to the ac (right) planes of the Ca2+-bound Syt1–SNARE complex in the long unit cell crystal form. The particular layer shown on the right corresponds to the red arrowhead in the left panel (only a slice corresponding to the layer is shown, creating the appearance of two disconnected groups of molecules—these groups are actually connected via interactions with the neighbouring layers). The red dashed oval indicates the ‘missing’ Syt1 C2AB fragment compared to the short unit cell crystal form (Extended Data Fig. 3d).
Extended Data Figure 3 Asymmetric unit, electron density maps and crystal packing of the Syt1–SNARE complex in the short unit cell crystal form.
a, Asymmetric unit of the Ca2+-bound Syt1–SNARE complex in the short unit cell crystal form at 3.6 Å resolution using diffraction data collected at the APS NE-CAT microfocus synchrotron beamline (Extended Data Table 1). The colour code is the same as in Fig. 1c. Two Syt1 C2AB fragments (distinguished by the designators I and I′) bind to the same SNARE complex in the asymmetric unit (see schema). b, mFo − DFc annealed omit map (Methods) of the Ca2+-bound Syt1–SNARE complex in the short unit cell crystal form collected at the APS NE-CAT microfocus synchrotron beamline; omitted residues within region I of the primary interface (residues 335–340 in Syt1 and 159–166 in SNAP-25) are coloured cyan. The contour level is 2.3σ . Left side, without B -factor sharpening; right side, with B -factor sharpening. c , Representative 2 mFo − DFc electron density map of the Ca2+-bound Syt1–SNARE complex for the short unit cell crystal form using diffraction data collected at the APS NE-CAT microfocus synchrotron beamline. The contour level is 1.5 σ . Left side, without B -factor sharpening; right side, with B -factor sharpening. b, c , The sharpening B -factor (−55 Å2) was set to make the lowest atomic B -factor of the short unit cell crystal form comparable to that of the long unit cell crystal form. Even with B -factor sharpening, the electron density map of the long unit cell crystal form collected at the LCLS XFEL is superior to that of the short unit cell crystal form collected at the APS NE-CAT microfocus synchrotron beamline. d , Views of the crystal lattice perpendicular to the bc (left) and to the ac (right) planes of the Ca2+-bound Syt1–SNARE complex in the short unit cell crystal form. The particular layer shown on the right corresponds to the red arrowhead in the left panel. The unit cell is outlined by a black box.
Extended Data Figure 4 Single-molecule FRET efficiency distributions of the Syt1–SNARE complex versus FRET efficiency values calculated from the Syt1–SNARE interfaces observed in the crystal structure.
Shown are histograms of intermolecular single molecule FRET (smFRET) efficiency values that were measured between pairs of covalently attached organic labels on the Syt1 C2AB fragment and the SNARE complex28 (also shown as large spheres superimposed on the interfaces observed in the crystal structure). Arrowheads indicate FRET efficiencies calculated from the crystal structure of the Ca2+-bound Syt1–SNARE complex in the long unit cell crystal form (complex I) for the primary, secondary and tertiary interfaces, using the methods and approximations described in ref. 28 to simulate the positions of dye centres in order to calculate the FRET-efficiency values. Only the dye pair combinations between the nearest C2 domain (including the C2A–C2B linker) and the SNARE complex were calculated for the three interfaces. Note that owing to the presence of transitions between different states the histograms reflect a combined effect of interaction interfaces. The label at position A61 would have disrupted the tertiary interfaces between the C2A domain and the SNARE complex, explaining the discrepancy for these labels (indicated by open triangles). In retrospect, the top smFRET-derived model28 and the primary interface observed in the crystal structure primarily differed in the orientation of the C2B domain. Moreover, the top smFRET-derived model predicted the approximate location of the primary interface on the neuronal SNARE (see Fig. 4c in ref. 28).
Extended Data Figure 5 Comparison of the two crystal forms and the Ca2+- and Mg2+-bound crystal structures of the Syt1–SNARE complex.
a, Superposition of the primary interfaces of the Ca2+-bound Syt1–SNARE complex structure in the long unit cell crystal form (gold and bright orange) and in the short unit cell crystal form (white). The primary interface is very similar in both crystal forms: the r.m.s.d. for the primary interface between both crystal forms is 0.38 Å (bright orange) and 0.42 Å (white) for complex I and complex II, respectively (including Cα atoms of the SNARE complex and the Syt1 C2B (I) domain forming the interface). b, Superposition of complex I in the long unit cell crystal form with the asymmetric unit of the short unit cell crystal form, but only showing the secondary interface (light-blue shaded disk) between Syt1 C2B (I′) and the SNARE complex (I). The bottom panels show close-up views of the secondary interface: left, interacting residues (sticks and balls); right, a 90° rotated view of the view shown in the left panel. The Syt1 C2B (I′) domain is rotated by 16° between the two crystal forms and, as a consequence, the interactions between residues R281, K288 and R398 of the Syt1 C2B (I′) domain and residues E224 and E228 of syntaxin-1A are slightly changed by this rotation. Notably, residues Syt1 R281, K288 and R398 are involved in both the primary (Fig. 2) and secondary interfaces. c, Superposition of complex I in the long unit cell crystal form with the asymmetric unit of the short unit cell crystal form, showing all interfaces. d, Superposition of the Ca2+-bound (white) and Mg2+-bound (black) crystal structures of the Syt1–SNARE complex, both in the short unit cell crystal form. The lower left panel shows a close-up view of the primary interface, indicating that it is very similar in both the Ca2+- and Mg2+-bound crystal structures. The Syt1 C2B domain that forms the secondary interface (light-blue shaded disk) is rotated by 19° between the Ca2+- and Mg2+-bound complexes. The lower-right panel is a rotated view of the complex, also showing the tertiary interface (light-green shaded disk), and the C2A–C2B interface that involves asymmetry-related Syt1 C2A domain (I′) (grey shaded disk). e, B-factor coloured cartoon representations of the asymmetric units of the Ca2+-bound long unit cell crystal form (top), the Ca2+-bound short unit cell crystal form (bottom left), and the Mg2+-bound short unit cell crystal form (bottom right) of the Syt1–SNARE complex. Note that the primary interfaces have relatively low B-factors, similar to the majority of the structure, while parts of the C2A and C2B domains involved in the secondary and tertiary interfaces have higher B-factors, possibly indicating increased flexibility.
Extended Data Figure 6 Sequence alignments of Syt1, SNAP-25 and syntaxin-1A from different homologues.
a, Sequence alignment of Syt1 homologues, showing the sequences around the primary interface of the Syt1–SNARE complex. Note that rat Syt5 refers to UniProt ID Q925C0, zebrafish Syt9 refers to GeneBank accession number AAI52175, rat Syt9 refers to UniProt ID P47861, and human Syt9 refers to UniProt ID O00445. b, Electrostatic potential surfaces of the known crystal structures of synaptotagmin-1, synaptotagmin-3, synaptotagmin-4 and synaptotagmin-7; the dashed rectangles indicate the regions that correspond to the primary interface regions I and II of the Syt1–SNARE complex. c, Sequence alignment of different SNAP-25 homologues, showing the sequences around the primary interface of the Syt1–SNARE complex. d, Sequence alignment of different syntaxin homologues, showing a sequence range around the primary interface of the Syt1–SNARE complex. In all panels, the interacting residues of the primary interface are indicated by solid circles and coloured boxes for region I (cyan) and region II (red/orange).
a, Top panels: CD spectra of wild-type and mutant Syt1 C2B domains in the absence of Ca2+. Bottom panels: thermal denaturation was monitored by molar ellipticity at a wavelength of 216 nm in the absence of Ca2+ (black) and in the presence of 5 mM Ca2+ (red). The specified melting temperatures were estimated as the mid-point of the melting curves (Methods). b, Superposition of the Syt1 C2B domains from the Ca2+-bound Syt1–SNARE complex in the short unit cell crystal form (gold), the crystal structure of the quintuple mutant (R281A/E295A/Y338W/R398A/R399A) of the Syt1 C2B domain (green), and the crystal structure of the isolated Syt1 C2B domain (white, PDB code 2YOA). c, d, Representative m2Fo − DFc electron density maps of the crystal structure of the quintuple mutant of the Syt1 C2B domain (Extended Data Table 1) contoured at 2.0σ. The labels refer to the mutated residues. e, Overlay of SEC profiles of full-length Syt1 mutant proteins used in the single vesicle–vesicle fusion assay (Fig. 3d–g). f, Coomassie-blue-stained SDS–PAGE with and without boiling of neuronal SNARE complexes formed by full-length SNAP-25 and its mutants, syntaxin-1A and synaptobrevin-2, using the proteins that were used in the single vesicle–vesicle fusion assay (Methods).
Extended Data Figure 8 Probability of fusion versus time upon 500 μM Ca2+ injection and spontaneous fusion for Syt1 and SNAP-25 mutants.
Shown are the data that were used to generate Fig. 3d–g. The number of independent experiments and analysed events are provided in Extended Data Table 2. a–d, Cumulative histograms of probability of fusion versus time for Syt1 mutants upon 500 μM Ca2+ injection (a) and spontaneous fusion (b), and SNAP-25 mutants upon 500 μM Ca2+ injection (c) and spontaneous fusion (d). e–g, Control experiments: e, Ca2+-triggered fusion; f, spontaneous fusion with 3 mM ATP, without SNAP-25 or Syt1; and g, mock injection without Ca2+.
The entire asymmetric unit of the long unit cell crystal form consists of two SNARE complexes and three Syt1 C2AB fragments. One of the two SNARE complexes interacts with two Syt1 C2AB fragments in the asymmetric unit, and a symmetry related C2AB fragment (designated as Complex I). The other SNARE complex just interacts with the C2B domain of one Syt1 C2AB fragment (designated as Complex II). The diffraction data for this crystal structure were collected at the X-ray free electron laser (XFEL) Linac Coherent Light Source (LCLS) at SLAC Accelerator Laboratory at Stanford University. (MOV 21214 kb)
At the start of the video, Complex I (long unit cell crystal form) is shown along with its symmetry mate, followed by close-up views of three different interfaces between Syt1 C2 domains and the SNARE complex, as well as the interface between two C2 domains. (MOV 28122 kb)
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Zhou, Q., Lai, Y., Bacaj, T. et al. Architecture of the synaptotagmin–SNARE machinery for neuronal exocytosis. Nature 525, 62–67 (2015). https://doi.org/10.1038/nature14975
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