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Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 Å resolution
Abstract
The evolutionarily conserved SNARE proteins and their complexes are involved in the fusion of vesicles with their target membranes; however, the overall organization and structural details of these complexes are unknown. Here we report the X-ray crystal structure at 2.4 A resolution of a core synaptic fusion complex containing syntaxin-1 A, synaptobrevin-II and SNAP-25B. The structure reveals a highly twisted and parallel four-helix bundle that differs from the bundles described for the haemagglutinin and HIV/SIV gp41 membrane-fusion proteins. Conserved leucine-zipper-like layers are found at the centre of the synaptic fusion complex. Embedded within these leucine-zipper layers is an ionic layer consisting of an arginine and three glutamine residues contributed from each of the four alpha-helices. These residues are highly conserved across the entire SNARE family. The regions flanking the leucine-zipper-like layers contain a hydrophobic core similar to that of more general four-helix-bundle proteins. The surface of the synaptic fusion complex is highly grooved and possesses distinct hydrophilic, hydrophobic and charged regions. These characteristics may be important for membrane fusion and for the binding of regulatory factors affecting neurotransmission.
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“Indeed modeling the four SNARE proteins (Ufe1, Use1, Sec20, and Sec22) that are known to mediate the fusion between Golgi-derived retrograde transport vesicles with ER (87), together resulted in a complex that resembles a typical SNARE complex (84) (fig. S26B, C).”
From Computed structures of core eukaryotic protein complexes (2021) · cites this paper as [84]
In the citing paper
“Membrane fusion requires the formation of a 4-helix bundle (called the SNARE complex) between the vesicle SNARE and the target membrane SNAREs (84,85).”
From Computed structures of core eukaryotic protein complexes (2021) · cites this paper as [84]
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“The coordinates for the SNARE complex were obtained from the crystal structure of the neuronal SNARE complex (PDB ID 1SFC) (Sutton et al., 1998) and those of the C2 domains of Syt1 from the Ca2+-free crystal structure of Syt1 (PDB ID 2R83) (Fuson et al.”
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“Despite their different sizes and structures among many organisms, the SNARE proteins share a conserved structure called the SNARE motif, which consists of 60–70 amino acids arranged in heptad repeats [7,8].”
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BackgroundSNARE Complex Regulation by Phosphorylation
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Tetrameric Hub Structure of Postsynaptic Scaffolding Protein Homer
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“The length of the coiled-coil domain is estimated to be 26 nm from the crystal structure of soluble N-ethylmaleimidesensitive factor attached protein receptor (SNARE) complex, a tetrameric coiled-coil (Sutton et al., 1998), which is beyond the efficient range of FRET ( 10 nm) (Fig.”
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The riddle of the Sec1/Munc-18 proteins – new twists added to their interactions with SNAREs
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Self-citationCombinatorial SNARE complexes modulate the secretion of cytoplasmic granules in human neutrophils
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“…membrane proteins along with NSF promote the physical linkage of juxtaposed membranes to atomic distances necessary for the subsequent coalescence of their respective phospholipid bilayers (Hanson et al., 1997; Woodman, 1997; Nichols and Pelham, 1998; Sutton et al., 1998; Skehel and Wiley, 1998).”
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“Fusion is initiated when the v-SNARE pairs with its cognate t-SNAREs to form a thermostable trans-SNARE complex (SNAREpin) that brings two membranes into close apposition to fuse (Söllner et al., 1993; Sutton et al., 1998; Weber et al., 1998; Hu et al., 2003; Wickner and Schekman, 2008).”
BackgroundMethodRat Basophilic Leukemia Cells Express Syntaxin-3 and VAMP-7 in Granule Membranes
Hibi, T., Hirashima, N., & Nakanishi, M. (2000) · Biochemical and Biophysical Research Communications · doi:10.1006/bbrc.2000.2591 · Cited by 99
Molecular Determinants of Syntaxin 1 Modulation of N-type Calcium Channels
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SNIP, a Novel SNAP-25-interacting Protein Implicated in Regulated Exocytosis
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Binding of Munc18-1 to Synaptobrevin and to the SNARE Four-Helix Bundle
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“In vitro studies of SNARE complex formation, together with the crystal structure of a plasma membrane SNARE complex, have revealed that the conserved coiled-coil regions of the SNAREs form a parallel four-helix bundle (Hanson et al., 1997; Sutton et al., 1998).”
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“The SNARE complex forms an extended parallel four-helix bundle in order to fuse the two membranes (Sutton et al., 1998; Antonin et al., 2002).”
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Self-citationMultiple SNARE interactions of an SM protein: Sed5p/Sly1p binding is dispensable for transport
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“Whereas SNAREs are type II membrane proteins that form helical bundles on opposing membranes to be fused (Sutton et al, 1998; Weber et al, 1998), Sec1/Munc18 family members are hydrophilic proteins that were first discovered in yeast.”
BackgroundInfluentialPalmitoylation of the synaptic vesicle fusion machinery
Prescott, G. R., Gorleku, O. A., Greaves, J., & Chamberlain, L. H. (2009) · Journal of Neurochemistry · doi:10.1111/j.1471-4159.2009.06205.x · Cited by 98
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“v-SNARE–t-SNARE pairing leads to coiled coil formation (39).”
BackgroundBiomarker-based dissection of neurodegenerative diseases
Olsson, B., Zetterberg, H., Hampel, H. J., & Blennow, K. (2011) · Progress in Neurobiology · doi:10.1016/j.pneurobio.2011.04.006 · Cited by 102
“STX1 is a component of the SNARE complex together with SNAP25 and synaptobrevin-2/VAMP2 (Sutton et al., 1998).”
BackgroundThe mechanisms of aquaporin control in the renal collecting duct
Klußmann, E., Maric, K., & Rosenthal, W. (2008) · Springer eBooks · doi:10.1007/bfb0119577 · Cited by 96
Graham, M. E., Fisher, R. J., & Burgoyne, R. D. (2000) · Biochimie · doi:10.1016/s0300-9084(00)00196-6 · Cited by 97
SNARE Complex Structure and Function
Hay, J. (2001) · Experimental Cell Research · doi:10.1006/excr.2001.5368 · Cited by 97
Yeast Golgi SNARE interactions are promiscuous
Tsui, M. M. K., & Banfield, D. K. (2000) · Journal of Cell Science · doi:10.1242/jcs.113.1.145 · Cited by 97
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“SNAP-25 contributes, together with syntaxin-1 (plasma membrane) and synaptobrevin (vesicular membrane), to the formation of the exocytotic fusion complex (Jahn and Fasshauer, 2012; Rizo and Rosenmund, 2008; Sutton et al., 1998).”
Membrane Fusion Induced by Small Molecules and Ions
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Exocytotic mechanism studied by truncated and zero layer mutants of the C‐terminus of SNAP‐25
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Volchuk, A., Ravazzola, M., Perrelet, A., et al. (2004) · Molecular Biology of the Cell · doi:10.1091/mbc.e03-08-0625 · Cited by 96
“The resulting SNAREpin, held together by a bundle of four -helices (Sutton et al., 1998), forcefully perturbs the apposing lipid bilayers, thereby triggering fusion (McNew et al., 2000b).”
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“The present study suggests that in exocytosis (and intracellular trafficking) the TM domains of SNARE proteins within a coiled-coil complex ( Sutton et al., 1998 ) are not only important for the formation of a fusion pore but also may be crucial for enlarging the pore to a size that allows passage of small molecules s…”
BackgroundAmyloid-β Oligomers May Impair SNARE-Mediated Exocytosis by Direct Binding to Syntaxin 1a
Yang, Y., Kim, J., Kim, H. Y., Ryoo, N., Lee, S., Kim, Y., Rhim, H., & Shin, Y.-K. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.07.044 · Cited by 88
“Our in vitro experiments not only reveal that Aβ binds to syntaxin 1a but further narrow the binding region to the SNARE motif, which forms a four-helix bundle (Poirier et al., 1998; Sutton et al., 1998).”
BackgroundComplexin arrests a pool of docked vesicles for fast Ca2+‐dependent release
Malsam, J., Parisotto, D. A., Bharat, T. A. M., Scheutzow, A., Krause, J. M., Briggs, J. A. G., & Söllner, T. H. (2012) · The EMBO Journal · doi:10.1038/emboj.2012.164 · Cited by 96
“…consisting of syntaxin 1 and SNAP-25 on the plasma membrane (So¨llner et al , 1993; and reviewed in Jahn and Scheller, 2006; Malsam et al , 2008). v-/t-SNARE complexes assemble via their heptad repeat-containing SNARE motifs into a four-helix bundle (Fasshauer et al , 1998; Sutton et al , 1998).”
Expression of the Longin domain of TI‐VAMP impairs lysosomal secretion and epithelial cell migration
Proux‐Gillardeaux, V., Raposo, G., Irinopoulou, T., & Galli, T. (2007) · Biology of the Cell · doi:10.1042/bc20060097 · Cited by 95
“…interactions and a ‘zero’ layer of hydrogen bonds between an arginine residue on the v-SNARE and three www.biolcell.org | Volume 99 (5) | Pages 261–271 261 V. Proux-Gillardeaux and others glutamine residues on the chains of two to three tSNAREs (Sutton et al., 1998; Antonin et al., 2002).”
BackgroundArachidonic acid potentiates exocytosis and allows neuronal SNARE complex to interact with Munc18a
Latham, C. F., Osborne, S. L., Cryle, M. J., & Meunier, F. A. (2006) · Journal of Neurochemistry · doi:10.1111/j.1471-4159.2006.04286.x · Cited by 95
Golgi reassembly after mitosis: The AAA family meets the ubiquitin family
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Munc18-1-regulated stage-wise SNARE assembly underlying synaptic exocytosis
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“The fully assembled SNARE complex forms a stable parallel four-helix bundle (Sutton et al., 1998; Stein et al., 2009)”
BackgroundMethodUnraveling the Mechanism of the Vesicle Transport ATPase NSF, the N-Ethylmaleimide-sensitive Factor
May, A. P., Whiteheart, S. W., & Weis, W. I. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.r100013200 · Cited by 95
The specificity of SNARE-dependent fusion is encoded in the SNARE motif
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Michaut, M. A., Tomes, C. N., Blas, G. A. D., Yunes, R., & Mayorga, L. S. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.180206197 · Cited by 94
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“Typical SNAREs contain a cytosolically exposed coiled-coil domain that is important for interacting with other SNAREs and that contributes to the specificity of the SNARE interactions (Sutton et al., 1998).”
BackgroundProgressive depletion of complexin II in a transgenic mouse model of Huntington's disease
Morton, A. J., & Edwardson, J. M. (2001) · Journal of Neurochemistry · doi:10.1046/j.1471-4159.2001.00059.x · Cited by 94
“The proteins studied included the synaptic vesicle membrane protein synaptobrevin and the plasma membrane proteins syntaxin and SNAP-25, known collectively as SNAREs, which form a tight complex between the two interacting membranes (Sutton et al. 1998).”
BackgroundRickman, C., Meunier, F. A., Binz, T., & Davletov, B. A. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m310879200 · Cited by 94
A Novel SNARE N-terminal Domain Revealed by the Crystal Structure of Sec22b
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Mechanism of arachidonic acid action on syntaxin–Munc18
Connell, E., Darios, F. D., Broersen, K., Gatsby, N., Peak‐Chew, S., Rickman, C., & Davletov, B. A. (2007) · EMBO Reports · doi:10.1038/sj.embor.7400935 · Cited by 94
“Syntaxins require Munc18 for conformational stabilization during transport and they initially will be in a tight union (Martinez-Arca et al, 2003; Toonen et al, 2005).”
BackgroundHrs regulates early endosome fusion by inhibiting formation of an endosomal SNARE complex
Sun, W., Yan, Q., Vida, T. A., & Bean, A. J. (2003) · The Journal of Cell Biology · doi:10.1083/jcb.200302083 · Cited by 94
“SNAP-25 is considered a Q-SNARE, predominantly expressed on the plasma membrane, that is involved in exocytosis (Fasshauer et al., 1998; Sutton et al., 1998; Jahn and Sudhof, 1999; Lin and Scheller, 2000; Chen and Scheller, 2001).”
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“Fusion of these vesicles is triggered by membrane depolarization and concomitant influx of Ca(2) ions and is dependent on the SNARE proteins synaptobrevin/VAMP 2, syntaxin 1, and SNAP-25, whose assembly into a highly stable SNARE complex (42) is thought to drive the fusion reaction (reviewed in references 20, 24, and…”
The SNARE Vti1a-β Is Localized to Small Synaptic Vesicles and Participates in a Novel SNARE Complex
Antonin, W., Riedel, D., & von Mollard, G. F. (2000) · Journal of Neuroscience · doi:10.1523/jneurosci.20-15-05724.2000 · Cited by 115
“Synaptobrevin and syntaxin contribute one helix and SNAP-25 two helices to a parallel four-helix bundle ( Sutton et al., 1998 ).”
BackgroundDeWitt, D. C., & Rhoades, E. R. (2013) · Biochemistry · doi:10.1021/bi4002369 · Cited by 93
Control of granule exocytosis in neutrophils
Lacy, P. (2008) · Frontiers in bioscience · doi:10.2741/3099 · Cited by 96
SV2B Regulates Synaptotagmin 1 by Direct Interaction
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Munc18-1 prevents the formation of ectopic SNARE complexes in living cells
Medine, C. N., Rickman, C., Chamberlain, L. H., & Duncan, R. R. (2007) · Journal of Cell Science · doi:10.1242/jcs.020230 · Cited by 93
“Membrane fusion requires the assembly of all three proteins into a trimeric, four-helical complex to promote fusion of the two opposing bilayers in living cells (Sutton et al., 1998; Burgoyne and Morgan, 2003; Sudhof, 1995).”
BackgroundApical targeting of syntaxin 3 is essential for epithelial cell polarity
Sharma, N., Low, S. H., Misra, S., Bhattaram, P., & Weimbs, T. (2006) · The Journal of Cell Biology · doi:10.1083/jcb.200603132 · Cited by 93
“Structural domains of syntaxin 3 were identifi ed by sequence alignment with the highly homologous syntaxin 1 whose structure has been previously reported (Fernandez et al., 1998; Sutton et al., 1998; Lerman et al., 2000; Misura et al., 2000).”
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Interactions between synaptic vesicle fusion proteins explored by atomic force microscopy
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“JCB • Volume 210 • NumBer 1 • 2015 136 four-helical bundle that catalyzes membrane fusion (Sutton et al., 1998).”
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Role of the synaptobrevin C terminus in fusion pore formation
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Ugo1 and Mdm30 act sequentially during Fzo1-mediated mitochondrial outer membrane fusion
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“This is in contrast to SNAREs tethering complexes, which are formed by parallel coiled-coil interactions, oriented parallel to the membrane surface and allowing closer membrane contacts (Sutton et al., 1998).”
ResultCellular Mechanisms for the Biogenesis and Transport of Synaptic and Dense-Core Vesicles
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Phorbol esters and neurotransmitter release: more than just protein kinase C?
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“…to the unprimed state, when the secretory apparatus is in the primed state (Figure 4e), the a helices of these three proteins are arranged as four intertwined tails, with SNAP-25 contributing two helices, the other two SNAREs contributing one helix each (see inset from Sutton et al., 1998).”
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NSF and p97/VCP: similar at first, different at last
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Arachidonic Acid Allows SNARE Complex Formation in the Presence of Munc18
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CFTR chloride channels are regulated by a SNAP-23/syntaxin 1A complex
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Spring-loaded unraveling of a single SNARE complex by NSF in one round of ATP turnover
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Mechanism of Substrate Recognition by Botulinum Neurotoxin Serotype A
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“The Q-SNARE motif of Syntaxin and SNAP-25 family proteins contains conserved layers of interacting amino acid side chains.”
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Exocytosis requires asymmetry in the central layer of the SNARE complex
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Moving the insulin-regulated glucose transporter GLUT4 into and out of storage
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A secretagogin locus of the mammalian hypothalamus controls stress hormone release
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“The priming of vesicular release is regulated by a multi-protein complex sequentially recruiting Ca2+ sensors, SNARE proteins and the docking machinery embedded in the presynaptic terminal (Hata et al, 1993; Sollner et al, 1993; Sutton et al, 1998; Pang & Sudhof, 2010).”
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Rab22a affects the morphology and function of the endocytic pathway
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“…available, but based on structural studies of the neuronal plasma membrane SNARE complex (Hanson et al., 1997; Lin and Scheller, 1997; Poirier et al., 1998; Sutton et al., 1998), it is likely to consist of a parallel four -helix bundle with all the SNARE transmembrane domains situated at one end.”
BackgroundMARCH-II Is a Syntaxin-6–binding Protein Involved in Endosomal Trafficking
Nakamura, N., Fukuda, H., Kato, A., & Hirose, S. (2005) · Molecular Biology of the Cell · doi:10.1091/mbc.e04-03-0216 · Cited by 88
“Only cognate pairs of SNAREs on transport vesicles (v-SNARE) and on target membranes (t-SNARE) form the SNARE complex through their conserved amphipathic helices (SNARE motifs) and draw two membranes into apposition, allowing membrane fusion to occur (Fasshauer et al., 1998; Sutton et al., 1998).”
Background
Metadata
- Authors
- Sutton, R. B., Fasshauer, D., Jahn, R., & Brunger, A. T.
- Affiliations
- Howard Hughes Medical Institute (US)
- Max Planck Society (DE)
- Venue
- Nature
- Published
- 1998-09
- Volume
- 395
- Issue
- 6700
- Pages
- 347-353
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W1822252127
- Semantic Scholar
- f0ea2581b47bed29546d2d208a47cff4312eb1fe
- Cited by
- 2,417
- References
- 52
- Citations by year
- 2026: 25 · 2025: 44 · 2024: 45 · 2023: 55 · 2022: 63 · 2021: 60 · 2020: 59 · 2019: 51 · 2018: 80 · 2017: 70 · 2016: 67 · 2015: 91 · 2014: 93 · 2013: 89 · 2012: 93
- FWCI
- 44.62
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
- Keywords
- SNARE complex, synaptic vesicle exocytosis, syntaxin 1A, membrane fusion, four-helix bundle, hydrophobic core, neurotransmitter release, vesicle fusion
- MeSH terms
- Antigens, Surface, Escherichia coli, Exocytosis, Membrane Fusion, Membrane Proteins, Models, Molecular, Nerve Tissue Proteins, Neurotoxins, Protein Binding, Protein Conformation, Recombinant Proteins, Synaptic Vesicles, Crystallography, X-Ray, Vesicular Transport Proteins, Macromolecular Substances, SNARE Proteins, R-SNARE Proteins, Synaptosomal-Associated Protein 25, Syntaxin 1
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