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- EMDB-44847: Tomograms of isolated synaptic vesicles from Syp-/- mouse brain -

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Entry
Database: EMDB / ID: EMD-44847
TitleTomograms of isolated synaptic vesicles from Syp-/- mouse brain
Map datatomogram of Syp-/- isolated synaptic vesicles
Sample
  • Organelle or cellular component: Mouse brain isolated glutamatergic synaptic vesicles
KeywordsV-ATPase / synaptic vesicle / MEMBRANE PROTEIN
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsWang C / Jiang W / Yang K / Wang X / Guo Q / Brunger AT
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)RO1MH63105 United States
CitationJournal: Nature / Year: 2024
Title: Structure and topography of the synaptic V-ATPase-synaptophysin complex.
Authors: Chuchu Wang / Wenhong Jiang / Jeremy Leitz / Kailu Yang / Luis Esquivies / Xing Wang / Xiaotao Shen / Richard G Held / Daniel J Adams / Tamara Basta / Lucas Hampton / Ruiqi Jian / Lihua ...Authors: Chuchu Wang / Wenhong Jiang / Jeremy Leitz / Kailu Yang / Luis Esquivies / Xing Wang / Xiaotao Shen / Richard G Held / Daniel J Adams / Tamara Basta / Lucas Hampton / Ruiqi Jian / Lihua Jiang / Michael H B Stowell / Wolfgang Baumeister / Qiang Guo / Axel T Brunger /
Abstract: Synaptic vesicles are organelles with a precisely defined protein and lipid composition, yet the molecular mechanisms for the biogenesis of synaptic vesicles are mainly unknown. Here we discovered a ...Synaptic vesicles are organelles with a precisely defined protein and lipid composition, yet the molecular mechanisms for the biogenesis of synaptic vesicles are mainly unknown. Here we discovered a well-defined interface between the synaptic vesicle V-ATPase and synaptophysin by in situ cryo-electron tomography and single-particle cryo-electron microscopy of functional synaptic vesicles isolated from mouse brains. The synaptic vesicle V-ATPase is an ATP-dependent proton pump that establishes the proton gradient across the synaptic vesicle, which in turn drives the uptake of neurotransmitters. Synaptophysin and its paralogues synaptoporin and synaptogyrin belong to a family of abundant synaptic vesicle proteins whose function is still unclear. We performed structural and functional studies of synaptophysin-knockout mice, confirming the identity of synaptophysin as an interaction partner with the V-ATPase. Although there is little change in the conformation of the V-ATPase upon interaction with synaptophysin, the presence of synaptophysin in synaptic vesicles profoundly affects the copy number of V-ATPases. This effect on the topography of synaptic vesicles suggests that synaptophysin assists in their biogenesis. In support of this model, we observed that synaptophysin-knockout mice exhibit severe seizure susceptibility, suggesting an imbalance of neurotransmitter release as a physiological consequence of the absence of synaptophysin.
History
DepositionMay 12, 2024-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44847.png

Downloads & links

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Map

FileDownload / File: emd_44847.map.gz / Format: CCP4 / Size: 262.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationtomogram of Syp-/- isolated synaptic vesicles
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.89 Å/pix.
x 187 pix.
= 1662.056 Å		8.89 Å/pix.
x 720 pix.
= 6399.36 Å		8.89 Å/pix.
x 511 pix.
= 4541.768 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: 8.888 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-142870016.0 - 221101520.0
Average (Standard dev.)16826844.0 (±31544906.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-94-2550
Dimensions720511187
Spacing511720187
CellA: 4541.7676 Å / B: 6399.36 Å / C: 1662.0559 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: tomogram of Syp-/- isolated synaptic vesicles

Fileemd_44847_additional_1.map
Annotationtomogram of Syp-/- isolated synaptic vesicles
Projections & Slices
AxesZYX

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Additional map: tomogram of Syp-/- isolated synaptic vesicles

Fileemd_44847_additional_10.map
Annotationtomogram of Syp-/- isolated synaptic vesicles
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: tomogram of Syp-/- isolated synaptic vesicles

Fileemd_44847_additional_2.map
Annotationtomogram of Syp-/- isolated synaptic vesicles
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AxesZYX

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Density Histograms

Histogram

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Additional map: tomogram of Syp-/- isolated synaptic vesicles

Fileemd_44847_additional_3.map
Annotationtomogram of Syp-/- isolated synaptic vesicles
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: tomogram of Syp-/- isolated synaptic vesicles

Fileemd_44847_additional_4.map
Annotationtomogram of Syp-/- isolated synaptic vesicles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: tomogram of Syp-/- isolated synaptic vesicles

Fileemd_44847_additional_5.map
Annotationtomogram of Syp-/- isolated synaptic vesicles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: tomogram of Syp-/- isolated synaptic vesicles

Fileemd_44847_additional_6.map
Annotationtomogram of Syp-/- isolated synaptic vesicles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: tomogram of Syp-/- isolated synaptic vesicles

Fileemd_44847_additional_7.map
Annotationtomogram of Syp-/- isolated synaptic vesicles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: tomogram of Syp-/- isolated synaptic vesicles

Fileemd_44847_additional_8.map
Annotationtomogram of Syp-/- isolated synaptic vesicles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: tomogram of Syp-/- isolated synaptic vesicles

Fileemd_44847_additional_9.map
Annotationtomogram of Syp-/- isolated synaptic vesicles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mouse brain isolated glutamatergic synaptic vesicles

EntireName: Mouse brain isolated glutamatergic synaptic vesicles
Components
  • Organelle or cellular component: Mouse brain isolated glutamatergic synaptic vesicles

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Supramolecule #1: Mouse brain isolated glutamatergic synaptic vesicles

SupramoleculeName: Mouse brain isolated glutamatergic synaptic vesicles / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Mus musculus (house mouse)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE
DetailsThe specimen state should be an intact subcellular component.
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 41

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT

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