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Structure paper

TitleStructure and topography of the synaptic V-ATPase-synaptophysin complex.
Journal, issue, pagesNature, Vol. 631, Issue 8022, Page 899-904, Year 2024
Publish dateJun 5, 2024
AuthorsChuchu Wang / Wenhong Jiang / Jeremy Leitz / Kailu Yang / Luis Esquivies / Xing Wang / Xiaotao Shen / Richard G Held / Daniel J Adams / Tamara Basta / Lucas Hampton / Ruiqi Jian / Lihua Jiang / Michael H B Stowell / Wolfgang Baumeister / Qiang Guo / Axel T Brunger /
PubMed AbstractSynaptic vesicles are organelles with a precisely defined protein and lipid composition, yet the molecular mechanisms for the biogenesis of synaptic vesicles are mainly unknown. Here we discovered a ...Synaptic vesicles are organelles with a precisely defined protein and lipid composition, 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. 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. Synaptophysin and its paralogues synaptoporin and synaptogyrin 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.
External linksNature / PubMed:38838737 / PubMed Central
MethodsEM (single particle) / EM (tomography) / EM (subtomogram averaging)
Resolution3.6 - 18.2 Å
Structure data

EMDB-44839, PDB-9bra:
Intact V-ATPase State 2 and synaptophysin complex in mouse brain isolated synaptic vesicles
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-44840, PDB-9brq:
Intact V-ATPase State 3 and synaptophysin complex in mouse brain isolated synaptic vesicles
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-44841, PDB-9brr:
Intact V-ATPase State 3 in synaptophysin knock-out isolated synaptic vesicles
Method: EM (single particle) / Resolution: 4.5 Å

EMDB-44842, PDB-9brs:
Intact V-ATPase State 2 in synaptophysin knock-out isolated synaptic vesicles
Method: EM (single particle) / Resolution: 4.4 Å

EMDB-44843, PDB-9brt:
Intact V-ATPase State 1 and synaptophysin complex in mouse brain isolated synaptic vesicles
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-44844, PDB-9bru:
Intact V-ATPase State 1 in synaptophysin knock-out isolated synaptic vesicles
Method: EM (single particle) / Resolution: 4.4 Å

EMDB-44845, PDB-9bry:
V0-only V-ATPase in synaptophysin gene knock-out mouse brain isolated synaptic vesicles
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-44846, PDB-9brz:
V0-only V-ATPase and synaptophysin complex in mouse brain isolated synaptic vesicles
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-44847: Tomograms of isolated synaptic vesicles from Syp-/- mouse brain
Method: EM (tomography)

EMDB-44848: Tomograms of isolated synaptic vesicles from wild-type mouse brain
Method: EM (tomography)

EMDB-44855: Intact state1 V-ATPase of isolated synaptic vesicles from wild-type mouse brain by subtomogram averaging
Method: EM (subtomogram averaging) / Resolution: 18.2 Å

EMDB-44856: Intact state2 V-ATPase of isolated synaptic vesicles from wild-type mouse brain by subtomogram averaging
Method: EM (subtomogram averaging) / Resolution: 15.9 Å

EMDB-44857: Intact state3 V-ATPase of isolated synaptic vesicles from wild-type mouse brain by subtomogram averaging
Method: EM (subtomogram averaging) / Resolution: 17.1 Å

EMDB-44858: V0-only V-ATPase of isolated synaptic vesicles from wild-type mouse brain by subtomogram averaging
Method: EM (subtomogram averaging) / Resolution: 16.0 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-BMA:
beta-D-mannopyranose

Source
  • mus musculus (house mouse)
KeywordsMEMBRANE PROTEIN / V-ATPase / synaptic vesicle / V0only V-ATPase

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