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- EMDB-11628: Distance-dependent synaptic vesicle protein organisation. -

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Basic information

Entry
Database: EMDB / ID: EMD-11628
TitleDistance-dependent synaptic vesicle protein organisation.
Map dataTomogram from delta-84 Munc-18 condition.
Sample
  • Complex: Synaptic membrane fusion reconstituted in vitro
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsGinger L / Malsam J / Sonnen AF-P / Morado D / Scheutzow A / Sollner TH / Briggs JAG
Funding support United Kingdom, Germany, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-CoG-648432 MEMBRANEFUSION United Kingdom
German Research Foundation (DFG)112927078 - TRR83 Germany
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
German Research Foundation (DFG)278001972 - TRR186 Germany
CitationJournal: FEBS Lett / Year: 2020
Title: Arrangements of proteins at reconstituted synaptic vesicle fusion sites depend on membrane separation.
Authors: Lucy Ginger / Joerg Malsam / Andreas F-P Sonnen / Dustin Morado / Andrea Scheutzow / Thomas H Söllner / John A G Briggs /
Abstract: Synaptic vesicle proteins, including N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs), Synaptotagmin-1 and Complexin, are responsible for controlling the synchronised fusion of ...Synaptic vesicle proteins, including N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs), Synaptotagmin-1 and Complexin, are responsible for controlling the synchronised fusion of synaptic vesicles with the presynaptic plasma membrane in response to elevated cytosolic calcium levels. A range of structures of SNAREs and their regulatory proteins have been elucidated, but the exact organisation of these proteins at synaptic junction membranes remains elusive. Here, we have used cryoelectron tomography to investigate the arrangement of synaptic proteins in an in vitro reconstituted fusion system. We found that the separation between vesicle and target membranes strongly correlates with the organisation of protein complexes at junctions. At larger membrane separations, protein complexes assume a 'clustered' distribution at the docking site, inducing a protrusion in the target membrane. As the membrane separation decreases, protein complexes become displaced radially outwards and assume a 'ring-like' arrangement. Our findings indicate that docked vesicles can possess a wide range of protein complex numbers and be heterogeneous in their protein arrangements.
History
DepositionAug 19, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateNov 18, 2020-
Current statusNov 18, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Movie viewer
Supplemental images

emd_11628.png

Downloads & links

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Map

FileDownload / File: emd_11628.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomogram from delta-84 Munc-18 condition.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.36 Å/pix.
x 928 pix.
= 4042.368 Å		4.36 Å/pix.
x 401 pix.
= 1746.756 Å		4.36 Å/pix.
x 960 pix.
= 4181.76 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 4.356 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-342.89383 - 323.2437
Average (Standard dev.)-0.04187934 (±9.39708)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-29900
Dimensions401960928
Spacing960401928
CellA: 4181.76 Å / B: 1746.756 Å / C: 4042.368 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.3564.3564.356
M x/y/z960401928
origin x/y/z0.0000.0000.000
length x/y/z4181.7601746.7564042.368
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS0-2990
NC/NR/NS960401928
D min/max/mean-342.894323.244-0.042

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Supplemental data

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Sample components

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Entire : Synaptic membrane fusion reconstituted in vitro

EntireName: Synaptic membrane fusion reconstituted in vitro
Components
  • Complex: Synaptic membrane fusion reconstituted in vitro

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Supramolecule #1: Synaptic membrane fusion reconstituted in vitro

SupramoleculeName: Synaptic membrane fusion reconstituted in vitro / type: complex / ID: 1 / Parent: 0
Details: Synaptic membrane fusion reconstituted in vitro by mixing: giant unilamellar vesicles reconstituted with t-SNARE complex proteins; small unilamellar vesicles reconstituted with v-SNARE and ...Details: Synaptic membrane fusion reconstituted in vitro by mixing: giant unilamellar vesicles reconstituted with t-SNARE complex proteins; small unilamellar vesicles reconstituted with v-SNARE and Synaptotagmin-1; Complexin-II and Munc-18.
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: BBI Solutions / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN 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: 1.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.0 µm / Nominal defocus min: 0.0 µm / Nominal magnification: 81000
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 reconstructionAlgorithm: BACK PROJECTION / Number images used: 121

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