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- EMDB-8808: Volta phase plate tomogram of SV(Cpx) + PM vesicle mixture -

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Basic information

Entry
Database: EMDB / ID: EMD-8808
TitleVolta phase plate tomogram of SV(Cpx) + PM vesicle mixture
Map dataTomogram of SV(Cpx) PM vesicle mixtures
Sample
  • Complex: Synaptic protein complexes
Biological speciesRattus norvegicus (Norway rat)
Methodelectron tomography / cryo EM
AuthorsGipson P
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Morphologies of synaptic protein membrane fusion interfaces.
Authors: Preeti Gipson / Yoshiyuki Fukuda / Radostin Danev / Ying Lai / Dong-Hua Chen / Wolfgang Baumeister / Axel T Brunger /
Abstract: Neurotransmitter release is orchestrated by synaptic proteins, such as SNAREs, synaptotagmin, and complexin, but the molecular mechanisms remain unclear. We visualized functionally active synaptic ...Neurotransmitter release is orchestrated by synaptic proteins, such as SNAREs, synaptotagmin, and complexin, but the molecular mechanisms remain unclear. We visualized functionally active synaptic proteins reconstituted into proteoliposomes and their interactions in a native membrane environment by electron cryotomography with a Volta phase plate for improved resolvability. The images revealed individual synaptic proteins and synaptic protein complex densities at prefusion contact sites between membranes. We observed distinct morphologies of individual synaptic proteins and their complexes. The minimal system, consisting of neuronal SNAREs and synaptotagmin-1, produced point and long-contact prefusion states. Morphologies and populations of these states changed as the regulatory factors complexin and Munc13 were added. Complexin increased the membrane separation, along with a higher propensity of point contacts. Further inclusion of the priming factor Munc13 exclusively restricted prefusion states to point contacts, all of which efficiently fused upon Ca triggering. We conclude that synaptic proteins have evolved to limit possible contact site assemblies and morphologies to those that promote fast Ca-triggered release.
History
DepositionJul 4, 2017-
Header (metadata) releaseAug 2, 2017-
Map releaseAug 2, 2017-
UpdateSep 6, 2017-
Current statusSep 6, 2017Processing site: RCSB / 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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  • Simplified surface model
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8808.png

Downloads & links

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Map

FileDownload / File: emd_8808.map.gz / Format: CCP4 / Size: 379.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomogram of SV(Cpx) PM vesicle mixtures
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.84 Å/pix.
x 117 pix.
= 800.28 Å		6.84 Å/pix.
x 825 pix.
= 5643. Å		6.84 Å/pix.
x 1031 pix.
= 7052.04 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: 6.84 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-3.8474927 - 7.743206
Average (Standard dev.)-0.0007023698 (±0.56256)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions8251031117
Spacing1031825117
CellA: 7052.04 Å / B: 5643.0 Å / C: 800.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.846.846.84
M x/y/z1031825117
origin x/y/z0.0000.0000.000
length x/y/z7052.0405643.000800.280
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS1031825117
D min/max/mean-3.8477.743-0.001

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Supplemental data

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Sample components

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Entire : Synaptic protein complexes

EntireName: Synaptic protein complexes
Components
  • Complex: Synaptic protein complexes

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Supramolecule #1: Synaptic protein complexes

SupramoleculeName: Synaptic protein complexes / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)

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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
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: EMdiasum / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 0.632 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 130

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