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- EMDB-52342: Short (SNARE complex dependent) synaptic vesicle tether -

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Basic information

Entry
Database: EMDB / ID: EMD-52342
TitleShort (SNARE complex dependent) synaptic vesicle tether
Map dataShort tether average
Sample
  • Organelle or cellular component: Synaptosome
    • Other: Putative neuronal SNARE complex (Syntaxin-1, SNAP25, Synaptobrevin-2) with Complexin-1 and Synptotagmin-1
KeywordsSNARE complex Presynaptic Synaptic vesicle tether Active zone complex Vesicle fusion Synaptic transmission / EXOCYTOSIS
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 31.2 Å
AuthorsLucic V / Oroczo-Borunda DH
Funding support France, 1 items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)RGP0020/2019 France
CitationJournal: Sci Adv / Year: 2023
Title: Munc13- and SNAP25-dependent molecular bridges play a key role in synaptic vesicle priming.
Authors: Christos Papantoniou / Ulrike Laugks / Julia Betzin / Cristina Capitanio / José Javier Ferrero / José Sánchez-Prieto / Susanne Schoch / Nils Brose / Wolfgang Baumeister / Benjamin H ...Authors: Christos Papantoniou / Ulrike Laugks / Julia Betzin / Cristina Capitanio / José Javier Ferrero / José Sánchez-Prieto / Susanne Schoch / Nils Brose / Wolfgang Baumeister / Benjamin H Cooper / Cordelia Imig / Vladan Lučić /
Abstract: Synaptic vesicle tethering, priming, and neurotransmitter release require a coordinated action of multiple protein complexes. While physiological experiments, interaction data, and structural studies ...Synaptic vesicle tethering, priming, and neurotransmitter release require a coordinated action of multiple protein complexes. While physiological experiments, interaction data, and structural studies of purified systems were essential for our understanding of the function of the individual complexes involved, they cannot resolve how the actions of individual complexes integrate. We used cryo-electron tomography to simultaneously image multiple presynaptic protein complexes and lipids at molecular resolution in their native composition, conformation, and environment. Our detailed morphological characterization suggests that sequential synaptic vesicle states precede neurotransmitter release, where Munc13-comprising bridges localize vesicles <10 nanometers and soluble -ethylmaleimide-sensitive factor attachment protein 25-comprising bridges <5 nanometers from the plasma membrane, the latter constituting a molecularly primed state. Munc13 activation supports the transition to the primed state via vesicle bridges to plasma membrane (tethers), while protein kinase C promotes the same transition by reducing vesicle interlinking. These findings exemplify a cellular function performed by an extended assembly comprising multiple molecularly diverse complexes.
History
DepositionDec 16, 2024-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52342.png

Downloads & links

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Map

FileDownload / File: emd_52342.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationShort tether average
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
8.78 Å/pix.
x 64 pix.
= 561.92 Å		8.78 Å/pix.
x 64 pix.
= 561.92 Å		8.78 Å/pix.
x 64 pix.
= 561.92 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-1.1522356 - 0.9421925
Average (Standard dev.)0.000029877332 (±0.018811222)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 561.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52342_msk_1.map
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Additional map: Short tether average without synaptic vesicle and plasma...

Fileemd_52342_additional_1.map
AnnotationShort tether average without synaptic vesicle and plasma membrane contributions
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Half map: Half 1

Fileemd_52342_half_map_1.map
AnnotationHalf 1
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Half map: Half 2

Fileemd_52342_half_map_2.map
AnnotationHalf 2
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Sample components

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Entire : Synaptosome

EntireName: Synaptosome
Components
  • Organelle or cellular component: Synaptosome
    • Other: Putative neuronal SNARE complex (Syntaxin-1, SNAP25, Synaptobrevin-2) with Complexin-1 and Synptotagmin-1

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Supramolecule #1: Synaptosome

SupramoleculeName: Synaptosome / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Synaptosomal fraction from rodent Hippocampus
Source (natural)Organism: Mus musculus (house mouse) / Strain: C57 B6/N / Organ: brain / Tissue: hippocampus / Location in cell: excitatory synapse
Molecular weightTheoretical: 132 KDa

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Macromolecule #1: Putative neuronal SNARE complex (Syntaxin-1, SNAP25, Synaptobrevi...

MacromoleculeName: Putative neuronal SNARE complex (Syntaxin-1, SNAP25, Synaptobrevin-2) with Complexin-1 and Synptotagmin-1
type: other / ID: 1
Details: Native, endogenous mammalian protein complex. Likely composed of neuronal SNARE complex (Syntaxin-1, SNAP25, Synaptobrevin-2) with Complexin-1 and Synptotagmin-1
Classification: other
Source (natural)Organism: Mus musculus (house mouse) / Strain: C57 B6/N / Organ: brain / Tissue: hippocampus
SequenceString:
MSATAATVPP AAPAGEGGPP APPPNLTSNR RLQQTQAQVD EVVDIMRVNV DKVLERDQKL SELDDRADAL QAGASQFETS AAKLKRKYWW KNLKMMIILG VICAIILIII IVYFST

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.4 / Component - Concentration: 300.0 mM / Component - Formula: HBM / Component - Name: Hepes-buffered medium
Details: 140 mM NaCl, 5 mM KCl, 5mM NaHCO3, 1.2 mM NaH2PO4-H2O, 1 mM MgCl26-H2O, 10 mM Glucose, 10 mM Hepes, 1.2 mM CaCl2
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: Portable manual plunger made at Max Planck Institute of Biochemistry.
DetailsSynaptosomal fraction (P2) was obtained from DIV 28-30 hippocampal organotypic slices.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 31.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number subtomograms used: 321
ExtractionNumber tomograms: 77 / Number images used: 321 / Method: Hierarchical connectivity / Software - Name: PyTo (ver. 1.10)
Details: Automatically detected bridges between synaptic vesicles and plasma membrane by hierarchical connectivity algorithm implemented in Pyto software
CTF correctionType: NONE
Final 3D classificationNumber classes: 1 / Avg.num./class: 321 / Software - Name: PyTo (ver. 1.10)
Details: All particles that were extracted were used for the final refinement and reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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