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- EMDB-44858: V0-only V-ATPase of isolated synaptic vesicles from wild-type mou... -

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Basic information

Entry
Database: EMDB / ID: EMD-44858
TitleV0-only V-ATPase of isolated synaptic vesicles from wild-type mouse brain by subtomogram averaging
Map data
Sample
  • Organelle or cellular component: Mouse brain isolated glutamatergic synaptic vesicles
KeywordsV-ATPase / synaptic vesicle / MEMBRANE PROTEIN
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 16.0 Å
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_44858.png

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Map

FileDownload / File: emd_44858.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
2.62 Å/pix.
x 96 pix.
= 251.52 Å		2.62 Å/pix.
x 96 pix.
= 251.52 Å		2.62 Å/pix.
x 96 pix.
= 251.52 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.62 Å
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Contour LevelBy AUTHOR: 0.114
Minimum - Maximum-0.3145215 - 0.47974116
Average (Standard dev.)0.008112283 (±0.06528089)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 251.51999 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: processed by M software

Fileemd_44858_additional_1.map
Annotationprocessed by M software
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Half map: #2

Fileemd_44858_half_map_1.map
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Half map: #1

Fileemd_44858_half_map_2.map
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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-#21
Source (natural)Organism: Mus musculus (house mouse)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE
DetailsThe specimen state should be an intact subcellular component.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 537
ExtractionNumber tomograms: 52 / Number images used: 1323
Final angle assignmentType: MAXIMUM LIKELIHOOD

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