9BRC

Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore D4A133 
Go to UniProtKB:  D4A133
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD4A133
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore P62815 
Go to UniProtKB:  P62815
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62815
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit C 1382Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q5FVI6 (Rattus norvegicus)
Explore Q5FVI6 
Go to UniProtKB:  Q5FVI6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5FVI6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATPase H+-transporting V1 subunit D247Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q6P503 (Rattus norvegicus)
Explore Q6P503 
Go to UniProtKB:  Q6P503
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P503
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit E 1
I, J, K
226Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q6PCU2 (Rattus norvegicus)
Explore Q6PCU2 
Go to UniProtKB:  Q6PCU2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PCU2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit F119Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P50408 (Rattus norvegicus)
Explore P50408 
Go to UniProtKB:  P50408
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50408
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit G
M, N, O
118Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q8R2H0 (Rattus norvegicus)
Explore Q8R2H0 
Go to UniProtKB:  Q8R2H0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8R2H0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit S1463Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for O54715 (Rattus norvegicus)
Explore O54715 
Go to UniProtKB:  O54715
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO54715
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Type IV secretion protein Dot
Q, R, S
573Legionella pneumophila subsp. pneumophilaMutation(s): 0 
Gene Names: lpg0968
UniProt
Find proteins for Q5ZWW6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZWW6 
Go to UniProtKB:  Q5ZWW6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZWW6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit H463Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for A0A8I5ZQ24 (Rattus norvegicus)
Explore A0A8I5ZQ24 
Go to UniProtKB:  A0A8I5ZQ24
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8I5ZQ24
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptophysin307Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P07825 (Rattus norvegicus)
Explore P07825 
Go to UniProtKB:  P07825
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07825
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase 116 kDa subunit a isoform 1V [auth a]838Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P25286 (Rattus norvegicus)
Explore P25286 
Go to UniProtKB:  P25286
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25286
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_aW [auth b]205Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for B0K022 (Rattus norvegicus)
Explore B0K022 
Go to UniProtKB:  B0K022
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0K022
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunitX [auth d]351Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q5M7T6 (Rattus norvegicus)
Explore Q5M7T6 
Go to UniProtKB:  Q5M7T6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5M7T6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit e 2Y [auth e]81Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q5EB76 (Rattus norvegicus)
Explore Q5EB76 
Go to UniProtKB:  Q5EB76
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5EB76
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Rnasek proteinZ [auth f]94Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for A0A8J8YMT9 (Rattus norvegicus)
Explore A0A8J8YMT9 
Go to UniProtKB:  A0A8J8YMT9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8J8YMT9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase 16 kDa proteolipid subunit c155Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P63081 (Rattus norvegicus)
Explore P63081 
Go to UniProtKB:  P63081
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63081
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Renin receptorJA [auth p]350Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q6AXS4 (Rattus norvegicus)
Explore Q6AXS4 
Go to UniProtKB:  Q6AXS4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6AXS4
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

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