PXD045356

PXD045356 is an original dataset announced via ProteomeXchange.

Title	Molecular architecture of individual synaptic vesicles
Description	Synaptic vesicles (SVs) perform neurotransmitter uptake inside the presynaptic neuron and their delivery to the synaptic cleft. The molecular composition of SVs was investigated, largely by proteomic analysis and fluorescent microscopy, and a model of an average SV was proposed. However, structural heterogeneity and molecular architecture of individual SVs are not yet well described. Here we used cryo-electron tomography (cryo-ET) to visualize morphological and molecular details of SVs isolated from native sources and inside synapses of cultured neurons. Surprisingly, a large fraction of the SV’s membrane did not show visible proteins. We describe several classes of small proteins on SVs' surface and long proteinaceous densities inside SVs. We identified large V-ATPases and determined their structure using subtomogram average (StA), and showed that it forms a complex with another membrane-embedded protein. Interestingly, V-ATPases were randomly distributed among the SVs irrespective of their sizes. We observed clathrin coats on a subpopulation of the SVs and partially assembled clathrin cages on isolated SVs and SVs inside cells. Finally, we describe non-vesicle-containing clathrin baskets, both from extracted SV preparations and within hippocampal neurons. Our analysis contributes to the understanding of the diversity of SVs and their molecular architecture.
HostingRepository	PRIDE
AnnounceDate	2025-03-17
AnnouncementXML	Submission_2025-03-17_07:17:32.354.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Max Ruwolt
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2023-09-13 09:22:16	ID requested
⏵ 1	2025-03-17 07:17:32	announced

10.1073/PNAS.2407375121;

submitter keyword: synaptic vesicles,SV, Fusion, ProteinaseK, Lumos, PK

Fan Liu
contact affiliation	Leibniz-Forschungsinstitut für Molekulare Pharmakologie
contact email	Fliu@fmp-berlin.de
lab head
Max Ruwolt
contact affiliation	Leibniz-Forschungsinstitut for Molecular Pharmacology
contact email	ruwolt@fmp-berlin.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PXD045356

PRIDE project URI

• PRIDE
  1. PXD045356
     1. Label: PRIDE project
     2. Name: Molecular architecture of individual synaptic vesicles