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- EMDB-44846: V0-only V-ATPase and synaptophysin complex in mouse brain isolate... -
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Open data
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Basic information
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Title | V0-only V-ATPase and synaptophysin complex in mouse brain isolated synaptic vesicles | |||||||||
![]() | Half map A of V0-only V-ATPasesynaptophysin complex in wild-type ISVs. | |||||||||
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![]() | V0only V-ATPase / ![]() ![]() | |||||||||
Function / homology | ![]() regulation of opioid receptor signaling pathway / Ion channel transport / Amino acids regulate mTORC1 / clathrin-sculpted glutamate transport vesicle membrane / Transferrin endocytosis and recycling / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | 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 Held / Daniel J Adams / Tamara Basta / Lucas Hampton / Ruiqi Jian / Lihua Jiang ...Authors: Chuchu Wang / Wenhong Jiang / Jeremy Leitz / Kailu Yang / Luis Esquivies / Xing Wang / Xiaotao Shen / Richard 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 protein gradient across the synaptic vesicle, which in turn drives the uptake of neurotransmitters. Synaptophysin and its paralogs 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. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 85.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 29.3 KB 29.3 KB | Display Display | ![]() |
Images | ![]() | 157.2 KB | ||
Filedesc metadata | ![]() | 8.1 KB | ||
Others | ![]() ![]() ![]() ![]() | 84.4 MB 71.3 MB 84.5 MB 84.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9brzMC ![]() 9braC ![]() 9brqC ![]() 9brrC ![]() 9brsC ![]() 9brtC ![]() 9bruC ![]() 9bryC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Half map A of V0-only V-ATPasesynaptophysin complex in wild-type ISVs. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.111 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_44846_additional_1.map | ||||||||||||
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-Additional map: Unsharpened map
File | emd_44846_additional_2.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
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Density Histograms |
-Half map: Half map A of V0-only V-ATPasesynaptophysin complex in...
File | emd_44846_half_map_1.map | ||||||||||||
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Annotation | Half map A of V0-only V-ATPasesynaptophysin complex in wild-type ISVs. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B of V0-only V-ATPasesynaptophysin complex in...
File | emd_44846_half_map_2.map | ||||||||||||
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Annotation | Half map B of V0-only V-ATPasesynaptophysin complex in wild-type ISVs. | ||||||||||||
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Density Histograms |
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Sample components
+Entire : Mouse brain isolated glutamatergic synaptic vesicles
+Supramolecule #1: Mouse brain isolated glutamatergic synaptic vesicles
+Macromolecule #1: V-type proton ATPase subunit S1
+Macromolecule #2: V-type proton ATPase 21 kDa proteolipid subunit c''
+Macromolecule #3: V-type proton ATPase subunit d 1
+Macromolecule #4: Ribonuclease kappa
+Macromolecule #5: V-type proton ATPase 16 kDa proteolipid subunit c
+Macromolecule #6: Renin receptor cytoplasmic fragment
+Macromolecule #7: Synaptophysin
+Macromolecule #8: V-type proton ATPase subunit e 2
+Macromolecule #9: V-type proton ATPase 116 kDa subunit a 1
+Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose
-Experimental details
-Structure determination
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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. |
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Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER |
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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42137 |
-Atomic model buiding 1
Details | Initial model: 6VQH, 6WLW, mouse synaptophysin from AlphaFold2 . For fitting and refinement details, see https://doi.org/10.1038/s41586-024-07610-x. |
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Refinement | Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-9brz: |