Subcellular Structures in Native Hippocampal Synapses Revealed by Cryo-electron Tomography

Synapses, the core components of neuronal circuits, rely on precise ultrastructural and molecular organization to facilitate quantal transmission and plasticity, which underpin brain information processing and storage. Cryo-electron tomography (cryo-ET) has emerged as a powerful tool for elucidating the nanoscale architecture of synapses, yet prior studies have largely focused on synaptic vesicles and postsynaptic receptors, leaving other critical components underexplored. Here, we employed cryo-ET to quantitatively analyze subcellular features across over 300 intact hippocampal synapses, revealing: (1) A significant proportion of excitatory synapses (32%) localized to dendritic shafts, while a relatively high proportion of inhibitory synapses targeted dendritic spines (35%), with synaptic clefts displaying four distinct geometries; (2) Diverse structures, including dense core vesicles, membraneless dense granules, and empty clathrin cages were enriched within presynaptic boutons; (3) Mitochondria prevalent in both pre- and postsynaptic regions, showing higher abundance of mitochondrial matrix granules postsynaptically. These findings provide a comprehensive view of the structural organization within hippocampal synapses and suggest fundamental principles governing their subcellular architecture.