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- EMDB-44848: Tomograms of isolated synaptic vesicles from wild-type mouse brain -
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Open data
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Basic information
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Title | Tomograms of isolated synaptic vesicles from wild-type mouse brain | |||||||||
![]() | tomogram of isolated synaptic vesicles from wild-type mouse brain | |||||||||
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![]() | V-ATPase / synaptic vesicle / MEMBRANE PROTEIN | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | electron tomography / cryo EM | |||||||||
![]() | Wang C / Jiang W / Yang K / Wang X / Guo Q / Brunger AT | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 242.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 29.2 KB 29.2 KB | Display Display | ![]() |
Images | ![]() | 154.7 KB | ||
Filedesc metadata | ![]() | 4.4 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 242.6 MB 242.7 MB 242.9 MB 242.6 MB 242.7 MB 225.6 MB 242.6 MB 242.6 MB 243.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | tomogram of isolated synaptic vesicles from wild-type mouse brain | ||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 8.888 Å | ||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: tomogram of isolated synaptic vesicles from wild-type mouse brain
File | emd_44848_additional_1.map | ||||||||||||
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Annotation | tomogram of isolated synaptic vesicles from wild-type mouse brain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: tomogram of isolated synaptic vesicles from wild-type mouse brain
File | emd_44848_additional_2.map | ||||||||||||
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Annotation | tomogram of isolated synaptic vesicles from wild-type mouse brain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: tomogram of isolated synaptic vesicles from wild-type mouse brain
File | emd_44848_additional_3.map | ||||||||||||
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Annotation | tomogram of isolated synaptic vesicles from wild-type mouse brain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: tomogram of isolated synaptic vesicles from wild-type mouse brain
File | emd_44848_additional_4.map | ||||||||||||
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Annotation | tomogram of isolated synaptic vesicles from wild-type mouse brain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: tomogram of isolated synaptic vesicles from wild-type mouse brain
File | emd_44848_additional_5.map | ||||||||||||
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Annotation | tomogram of isolated synaptic vesicles from wild-type mouse brain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: tomogram of isolated synaptic vesicles from wild-type mouse brain
File | emd_44848_additional_6.map | ||||||||||||
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Annotation | tomogram of isolated synaptic vesicles from wild-type mouse brain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: tomogram of isolated synaptic vesicles from wild-type mouse brain
File | emd_44848_additional_7.map | ||||||||||||
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Annotation | tomogram of isolated synaptic vesicles from wild-type mouse brain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: tomogram of isolated synaptic vesicles from wild-type mouse brain
File | emd_44848_additional_8.map | ||||||||||||
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Annotation | tomogram of isolated synaptic vesicles from wild-type mouse brain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: tomogram of isolated synaptic vesicles from wild-type mouse brain
File | emd_44848_additional_9.map | ||||||||||||
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Annotation | tomogram of isolated synaptic vesicles from wild-type mouse brain | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Mouse brain isolated glutamatergic synaptic vesicles
Entire | Name: Mouse brain isolated glutamatergic synaptic vesicles |
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Components |
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-Supramolecule #1: Mouse brain isolated glutamatergic synaptic vesicles
Supramolecule | Name: Mouse brain isolated glutamatergic synaptic vesicles / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#9 |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | electron tomography |
Aggregation state | cell |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
Details | The specimen state should be an intact subcellular component. |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: EMS / Diameter: 10 nm |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 reconstruction | Number images used: 41 |
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-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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