9BRA

Intact V-ATPase State 2 and synaptophysin complex in mouse brain isolated synaptic vesicles


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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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.Adams, D.J.Basta, T.Hampton, L.Jian, R.Jiang, L.Stowell, M.H.B.Baumeister, W.Guo, Q.Brunger, A.T.

(2024) Nature 

  • 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 E 1A [auth 8],
C [auth 9],
E [auth Q]
226Mus musculusMutation(s): 0 
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IMPC:  MGI:894326
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit G 2B [auth R],
D [auth T],
F [auth V]
118Mus musculusMutation(s): 0 
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IMPC:  MGI:1913487
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase catalytic subunit AG [auth 0],
H [auth 1],
I [auth 2]
617Mus musculusMutation(s): 0 
EC: 7.1.2.2
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IMPC:  MGI:1201780
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit B, brain isoformJ [auth 3],
K [auth 4],
L [auth 5]
511Mus musculusMutation(s): 0 
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IMPC:  MGI:109618
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit C 1M [auth 6]382Mus musculusMutation(s): 0 
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IMPC:  MGI:1913585
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit DN [auth 7]247Mus musculusMutation(s): 0 
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IMPC:  MGI:1921084
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit HO [auth U]483Mus musculusMutation(s): 0 
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IMPC:  MGI:1914864
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit FP [auth X]119Mus musculusMutation(s): 0 
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IMPC:  MGI:1913394
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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 
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IMPC:  MGI:103286
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase 21 kDa proteolipid subunit c''R [auth b]205Mus musculusMutation(s): 0 
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IMPC:  MGI:1890510
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit d 1S [auth d]351Mus musculusMutation(s): 0 
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IMPC:  MGI:1201778
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase 16 kDa proteolipid subunit c155Mus musculusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Renin receptor cytoplasmic fragmentCA [auth p]350Mus musculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit S1DA [auth c]463Mus musculusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease kappaEA [auth f]98Mus musculusMutation(s): 0 
EC: 3.1
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IMPC:  MGI:106369
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
SynaptophysinFA [auth s]314Mus musculusMutation(s): 0 
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IMPC:  MGI:98467
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit e 2GA [auth e]81Mus musculusMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 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