9B8Q | pdb_00009b8q

Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, peripheral stalks


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

High-resolution electron cryomicroscopy of V-ATPase in native synaptic vesicles.

Coupland, C.E.Karimi, R.Bueler, S.A.Liang, Y.Courbon, G.M.Di Trani, J.M.Wong, C.J.Saghian, R.Youn, J.Y.Wang, L.Y.Rubinstein, J.L.

(2024) Science 385: 168-174

  • DOI: https://doi.org/10.1126/science.adp5577
  • Primary Citation of Related Structures:  
    9B8O, 9B8P, 9B8Q, 9BRB, 9BRC, 9BRD

  • PubMed Abstract: 

    Intercellular communication in the nervous system occurs through the release of neurotransmitters into the synaptic cleft between neurons. In the presynaptic neuron, the proton pumping vesicular- or vacuolar-type ATPase (V-ATPase) powers neurotransmitter loading into synaptic vesicles (SVs), with the V 1 complex dissociating from the membrane region of the enzyme before exocytosis. We isolated SVs from rat brain using SidK, a V-ATPase-binding bacterial effector protein. Single particle electron cryomicroscopy allowed high-resolution structure determination of V-ATPase within the native SV membrane. In the structure, regularly spaced cholesterol molecules decorate the enzyme's rotor and the abundant SV protein synaptophysin binds the complex stoichiometrically. ATP hydrolysis during vesicle loading results in loss of V 1 from the SV membrane, suggesting that loading is sufficient to induce dissociation of the enzyme.


  • Organizational Affiliation
    • Molecular Medicine Program, The Hospital for Sick Children, Toronto, Canada M5G 1X8.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit C 1A [auth G]382Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q5FVI6 (Rattus norvegicus)
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Go to UniProtKB:  Q5FVI6
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UniProt GroupQ5FVI6
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit E 1B [auth I],
C [auth J],
D [auth K]
226Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q6PCU2 (Rattus norvegicus)
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UniProt GroupQ6PCU2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit GE [auth M],
F [auth N],
G [auth O]
118Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q8R2H0 (Rattus norvegicus)
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UniProt GroupQ8R2H0
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit HH [auth T]483Rattus norvegicusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase 116 kDa subunit a isoform 1I [auth a]838Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P25286 (Rattus norvegicus)
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UniProt GroupP25286
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaPJT166152

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Data collection, Database references
  • Version 1.2: 2024-07-24
    Changes: Data collection, Database references