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- EMDB-44845: V0-only V-ATPase in synaptophysin gene knock-out mouse brain isol... -
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Open data
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Basic information
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Title | V0-only V-ATPase in synaptophysin gene knock-out mouse brain isolated synaptic vesicles | |||||||||
![]() | Full map of V0-only V-ATPase in SYP-KO ISVs. | |||||||||
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![]() | V0only V-ATPase / synaptic vesicle / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() Ion channel transport / Amino acids regulate mTORC1 / Transferrin endocytosis and recycling / Insulin receptor recycling / eye pigmentation / RHOA GTPase cycle / central nervous system maturation / Metabolism of Angiotensinogen to Angiotensins / transporter activator activity / negative regulation of autophagic cell death ...Ion channel transport / Amino acids regulate mTORC1 / Transferrin endocytosis and recycling / Insulin receptor recycling / eye pigmentation / RHOA GTPase cycle / central nervous system maturation / Metabolism of Angiotensinogen to Angiotensins / transporter activator activity / negative regulation of autophagic cell death / plasma membrane proton-transporting V-type ATPase complex / rostrocaudal neural tube patterning / cellular response to increased oxygen levels / positive regulation of transforming growth factor beta1 production / synaptic vesicle lumen acidification / intracellular organelle / ROS and RNS production in phagocytes / proton-transporting V-type ATPase, V0 domain / P-type proton-exporting transporter activity / endosome to plasma membrane protein transport / lysosomal lumen acidification / clathrin-coated vesicle membrane / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar transport / proton-transporting V-type ATPase complex / head morphogenesis / osteoclast development / vacuolar proton-transporting V-type ATPase complex / dendritic spine membrane / regulation of cellular pH / vacuolar acidification / autophagosome membrane / regulation of MAPK cascade / ATPase activator activity / positive regulation of Wnt signaling pathway / cilium assembly / transmembrane transporter complex / endomembrane system / regulation of macroautophagy / angiotensin maturation / axon terminus / RNA endonuclease activity / proton-transporting ATPase activity, rotational mechanism / Neutrophil degranulation / proton transmembrane transport / endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis / transmembrane transport / small GTPase binding / synaptic vesicle membrane / positive regulation of canonical Wnt signaling pathway / melanosome / synaptic vesicle / signaling receptor activity / ATPase binding / cell body / postsynaptic membrane / intracellular iron ion homeostasis / receptor-mediated endocytosis of virus by host cell / Hydrolases; Acting on ester bonds / positive regulation of ERK1 and ERK2 cascade / early endosome / endosome membrane / endosome / nuclear speck / apical plasma membrane / external side of plasma membrane / axon / lysosomal membrane / centrosome / ubiquitin protein ligase binding / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / extracellular space / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | 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 | ![]() | 86.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 28.3 KB 28.3 KB | Display Display | ![]() |
Images | ![]() | 156.9 KB | ||
Filedesc metadata | ![]() | 7.8 KB | ||
Others | ![]() ![]() ![]() ![]() | 81.9 MB 71.3 MB 84.5 MB 84.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9bryMC ![]() 9braC ![]() 9brqC ![]() 9brrC ![]() 9brsC ![]() 9brtC ![]() 9bruC ![]() 9brzC 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
File | ![]() | ||||||||||||||||||||
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Annotation | Full map of V0-only V-ATPase in SYP-KO ISVs. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.1064 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: EMhancer full map of V0-only V-ATPase in SYP-KO ISVs.
File | emd_44845_additional_1.map | ||||||||||||
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Annotation | EMhancer full map of V0-only V-ATPase in SYP-KO ISVs. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_44845_additional_2.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B of V0-only V-ATPase in SYP-KO ISVs.
File | emd_44845_half_map_1.map | ||||||||||||
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Annotation | Half map B of V0-only V-ATPase in SYP-KO ISVs. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A of V0-only V-ATPase in SYP-KO ISVs.
File | emd_44845_half_map_2.map | ||||||||||||
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Annotation | Half map A of V0-only V-ATPase in SYP-KO ISVs. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Syptophysin gene knock-out mouse brain isolated glutamatergic syn...
+Supramolecule #1: Syptophysin gene knock-out mouse brain isolated glutamatergic syn...
+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: V-type proton ATPase subunit e 2
+Macromolecule #8: V-type proton ATPase 116 kDa subunit a 1
+Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #12: beta-D-mannopyranose
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
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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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
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53390 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Details | The initial model is the model of wild-type V0-only V-ATPase. 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-9bry: |