9BRY | pdb_00009bry

V0-only V-ATPase in synaptophysin gene knock-out mouse brain isolated synaptic vesicles


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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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 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: 407.29 kDa 
  • Atom Count: 23,530 
  • Modeled Residue Count: 3,066 
  • Deposited Residue Count: 3,721 
  • Unique protein chains: 8

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)
Explore Q9R1Q9 
Go to UniProtKB:  Q9R1Q9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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)
Explore Q91V37 
Go to UniProtKB:  Q91V37
IMPC:  MGI:1890510
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91V37
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Reference Sequence
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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)
Explore P51863 
Go to UniProtKB:  P51863
IMPC:  MGI:1201778
Entity Groups
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UniProt GroupP51863
Sequence Annotations
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Reference Sequence
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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
Find proteins for Q8K3C0 (Mus musculus)
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Go to UniProtKB:  Q8K3C0
IMPC:  MGI:106369
Entity Groups
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UniProt GroupQ8K3C0
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Reference Sequence
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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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Go to UniProtKB:  P63082
Entity Groups
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UniProt GroupP63082
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Renin receptor cytoplasmic fragmentN [auth p]290Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CYN9 (Mus musculus)
Explore Q9CYN9 
Go to UniProtKB:  Q9CYN9
Entity Groups
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UniProt GroupQ9CYN9
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit e 2O [auth e]81Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q91XE7 (Mus musculus)
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Go to UniProtKB:  Q91XE7
IMPC:  MGI:1923502
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UniProt GroupQ91XE7
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase 116 kDa subunit a 1P [auth a]838Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Z1G4 (Mus musculus)
Explore Q9Z1G4 
Go to UniProtKB:  Q9Z1G4
IMPC:  MGI:103286
Entity Groups
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UniProt GroupQ9Z1G4
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD 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-glucopyranoseQ [auth A]3N-Glycosylation
Glycosylation Resources
GlyTouCan: G47362BJ
GlyCosmos: G47362BJ
GlyGen: G47362BJ
Entity ID: 10
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseR [auth B],
S [auth C]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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
  • Version 1.2: 2024-11-20
    Changes: Data collection, Structure summary