9B8O image
Deposition Date 2024-03-31
Release Date 2024-06-26
Last Version Date 2024-10-23
Entry Detail
PDB ID:
9B8O
Title:
Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:ATPase H+-transporting V1 subunit D
Gene (Uniprot):Atp6v1d
Chain IDs:A (auth: H)
Chain Length:155
Number of Molecules:1
Biological Source:Rattus norvegicus
Polymer Type:polypeptide(L)
Molecule:V-type proton ATPase subunit F
Gene (Uniprot):Atp6v1f
Chain IDs:S (auth: L)
Chain Length:155
Number of Molecules:1
Biological Source:Rattus norvegicus
Polymer Type:polypeptide(L)
Molecule:V-type proton ATPase subunit S1
Gene (Uniprot):Atp6ap1
Chain IDs:B (auth: P)
Chain Length:350
Number of Molecules:1
Biological Source:Rattus norvegicus
Polymer Type:polypeptide(L)
Molecule:Synaptophysin
Gene (Uniprot):Syp
Chain IDs:C (auth: U)
Chain Length:307
Number of Molecules:1
Biological Source:Rattus norvegicus
Polymer Type:polypeptide(L)
Molecule:V-type proton ATPase 116 kDa subunit a 1
Gene (Uniprot):Atp6v0a1
Chain IDs:D (auth: a)
Chain Length:826
Number of Molecules:1
Biological Source:Rattus norvegicus
Polymer Type:polypeptide(L)
Molecule:ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a
Gene (Uniprot):Atp6v0b
Chain IDs:E (auth: b)
Chain Length:205
Number of Molecules:1
Biological Source:Rattus norvegicus
Polymer Type:polypeptide(L)
Molecule:V-type proton ATPase subunit
Gene (Uniprot):Atp6v0d1
Chain IDs:F (auth: d)
Chain Length:351
Number of Molecules:1
Biological Source:Rattus norvegicus
Polymer Type:polypeptide(L)
Molecule:V-type proton ATPase subunit e 2
Gene (Uniprot):Atp6v0e2
Chain IDs:G (auth: e)
Chain Length:81
Number of Molecules:1
Biological Source:Rattus norvegicus
Polymer Type:polypeptide(L)
Molecule:Rnasek protein
Gene (Uniprot):Rnasek
Chain IDs:H (auth: f)
Chain Length:86
Number of Molecules:1
Biological Source:Rattus norvegicus
Polymer Type:polypeptide(L)
Molecule:V-type proton ATPase 16 kDa proteolipid subunit c
Gene (Uniprot):Atp6v0c
Chain IDs:I (auth: g), J (auth: h), K (auth: i), L (auth: j), M (auth: k), N (auth: l), O (auth: m), P (auth: n), Q (auth: o)
Chain Length:155
Number of Molecules:9
Biological Source:Rattus norvegicus
Polymer Type:polypeptide(L)
Molecule:Renin receptor
Gene (Uniprot):Atp6ap2
Chain IDs:R (auth: p)
Chain Length:350
Number of Molecules:1
Biological Source:Rattus norvegicus
Primary Citation
High-resolution electron cryomicroscopy of V-ATPase in native synaptic vesicles.
Science 385 168 174 (2024)
PMID: 38900912 DOI: 10.1126/science.adp5577

Abstact

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 V1 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 a loss of the V1 region of V-ATPase from the SV membrane, suggesting that loading is sufficient to induce dissociation of the enzyme.

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Primary Citation of related structures