Chong‑Li Tian1,2  · Lei Qi1,3  · Zhen‑Hang Lu1,2  · Shuo Liu2,4  · Min‑Ling Gu1,2  · Wen‑Lan Huang2  · Yi‑Tong Yan1,2  · Yun‑Tao Liu5,6  · Jing Wu7  · Peiyi Wang7,8  · Z. Hong Zhou5,6  · Guo‑Qiang Bi1,2,3  · Pak‑Ming Lau1,2,3  · Chang‑Lu Tao1,2,4

1 MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, Center for Integrative Imaging, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China 

2 Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen–Hong Kong Institute of Brain Science, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China 

3 Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Hefei Comprehensive National Science Center, Institute of Artificial Intelligence, Hefei 230088, China 

4 Faculty of Life Sciences, Shenzhen University of Advanced Technology, Shenzhen 518107, China 

5 California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA 

6 Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA 

7 Cryo‑EM Centre, Southern University of Science and Technology, Shenzhen 518055, China 

8 Present Address: Cryo‑EM Center, Shandong Agricultural University, Taian 271018, China

Abstract

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.

Keywords

Neuronal synapses; Dense core vesicles; Dense granules; Clathrin cages; Mitochondrial matrix granules; Cryo-electron tomography

[SpringerLink]