9BRZ

V0-only V-ATPase and synaptophysin complex in mouse brain isolated synaptic vesicles


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and topography of the synaptic V-ATPase-synaptophysin complex.

Wang, C.Jiang, W.Leitz, J.Yang, K.Esquivies, L.Wang, X.Shen, X.Held, R.G.Adams, D.J.Basta, T.Hampton, L.Jian, R.Jiang, L.Stowell, M.H.B.Baumeister, W.Guo, Q.Brunger, A.T.

(2024) Nature 631: 899-904

  • DOI: https://doi.org/10.1038/s41586-024-07610-x
  • Primary Citation of Related Structures:  
    9BRA, 9BRQ, 9BRR, 9BRS, 9BRT, 9BRU, 9BRY, 9BRZ

  • PubMed Abstract: 

    Synaptic vesicles are organelles with a precisely defined protein and lipid composition 1,2 , 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 3 . 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 4,5 . Synaptophysin 6 and its paralogs synaptoporin 7 and synaptogyrin 8 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.


  • Organizational Affiliation

    Department of Molecular and Cellular Physiology, Stanford University, Stanford, California, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit S1A [auth c]463Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9R1Q9 (Mus musculus)
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Go to UniProtKB:  Q9R1Q9
Entity Groups  
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UniProt GroupQ9R1Q9
Glycosylation
Glycosylation Sites: 7Go to GlyGen: Q9R1Q9-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase 21 kDa proteolipid subunit c''B [auth b]205Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q91V37 (Mus musculus)
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Go to UniProtKB:  Q91V37
IMPC:  MGI:1890510
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UniProt GroupQ91V37
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit d 1C [auth d]351Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P51863 (Mus musculus)
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IMPC:  MGI:1201778
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UniProt GroupP51863
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease kappaD [auth f]98Mus musculusMutation(s): 0 
EC: 3.1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
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IMPC:  MGI:106369
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UniProt GroupQ8K3C0
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase 16 kDa proteolipid subunit c155Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P63082 (Mus musculus)
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UniProt GroupP63082
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Renin receptor cytoplasmic fragmentN [auth p]350Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CYN9 (Mus musculus)
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UniProt GroupQ9CYN9
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
SynaptophysinO [auth s]314Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q62277 (Mus musculus)
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IMPC:  MGI:98467
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit e 2P [auth e]81Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q91XE7 (Mus musculus)
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IMPC:  MGI:1923502
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UniProt GroupQ91XE7
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase 116 kDa subunit a 1Q [auth a]838Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9Z1G4 (Mus musculus)
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IMPC:  MGI:103286
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UniProt GroupQ9Z1G4
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Oligosaccharides

Help

Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseR [auth A]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G47362BJ
GlyCosmos:  G47362BJ
GlyGen:  G47362BJ
Entity ID: 11
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseS [auth B],
T [auth C],
U [auth D]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesRO1MH63105

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release
  • Version 1.1: 2024-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary