9BRQ | pdb_00009brq

Intact V-ATPase State 3 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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This is version 1.1 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 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 proton gradient across the synaptic vesicle, which in turn drives the uptake of neurotransmitters 4,5 . Synaptophysin 6 and its paralogues 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, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 1,081.5 kDa 
  • Atom Count: 67,167 
  • Modeled Residue Count: 8,590 
  • Deposited Residue Count: 9,742 
  • Unique protein chains: 17

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase 21 kDa proteolipid subunit c''A [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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IMPC:  MGI:1890510
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UniProt GroupQ91V37
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Reference Sequence
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Entity ID: 2
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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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase catalytic subunit ADA [auth 0],
K [auth 1],
L [auth 2]
617Mus musculusMutation(s): 0 
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P50516 (Mus musculus)
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IMPC:  MGI:1201780
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UniProt GroupP50516
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit B, brain isoformM [auth 3],
N [auth 4],
O [auth 5]
511Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P62814 (Mus musculus)
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IMPC:  MGI:109618
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UniProt GroupP62814
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit DP [auth 7]247Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P57746 (Mus musculus)
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IMPC:  MGI:1921084
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UniProt GroupP57746
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit E 1Q [auth 8],
R [auth 9],
S [auth Q]
226Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P50518 (Mus musculus)
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IMPC:  MGI:894326
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UniProt GroupP50518
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit G 2T [auth R],
U [auth T],
V
118Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9WTT4 (Mus musculus)
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IMPC:  MGI:1913487
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit FW [auth X]119Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9D1K2 (Mus musculus)
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IMPC:  MGI:1913394
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit C 1X [auth 6]382Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9Z1G3 (Mus musculus)
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IMPC:  MGI:1913585
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit HY [auth U]483Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q8BVE3 (Mus musculus)
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IMPC:  MGI:1914864
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit d 1Z [auth d]351Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P51863 (Mus musculus)
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IMPC:  MGI:1201778
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase 116 kDa subunit a 1AA [auth a]838Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:103286
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit S1BA [auth c]463Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9R1Q9 (Mus musculus)
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Renin receptor cytoplasmic fragmentCA [auth p]350Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CYN9 (Mus musculus)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribonuclease kappaEA [auth f]98Mus musculusMutation(s): 0 
EC: 3.1
Membrane Entity: Yes 
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IMPC:  MGI:106369
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
SynaptophysinFA [auth s]314Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q62277 (Mus musculus)
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IMPC:  MGI:98467
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit e 2GA [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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Reference Sequence

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

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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