9B8P

Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 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
H(+)-transporting two-sector ATPase
A, B, C
647Rattus norvegicusMutation(s): 0 
EC: 7.1.2.2
UniProt
Find proteins for D4A133 (Rattus norvegicus)
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UniProt GroupD4A133
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit B, brain isoform
D, E, F
511Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P62815 (Rattus norvegicus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATPase H+-transporting V1 subunit DG [auth H]247Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q6P503 (Rattus norvegicus)
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UniProt GroupQ6P503
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit E 1H [auth I],
I [auth J],
J [auth K]
226Rattus norvegicusMutation(s): 0 
UniProt
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UniProt GroupQ6PCU2
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit FK [auth L]119Rattus norvegicusMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit GL [auth M],
M [auth N],
N [auth O]
118Rattus norvegicusMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
SidKO [auth Q],
P [auth R],
Q [auth S]
573Legionella pneumophila subsp. pneumophila str. Philadelphia 1Mutation(s): 0 
Gene Names: lpg0968
UniProt
Find proteins for Q5ZWW6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
R [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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: 2024-07-03
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Data collection, Database references