Near‐atomic resolution structure of a plant geminivirus determined by electron cryo‐microscopy

African cassava mosaic virus belongs to the begomovirus genus of the geminivirus family. The unique twin particles of incomplete icosahedra are joined at five‐fold vertices building an unusual waist. The interaction within a half‐capsid or across the waist was unknown so far. We have determined the virion structure by electron cryo‐microscopy with a resolution of 4.2 Å and built an atomic model for its capsid protein. The inter‐capsomer contacts mediated by the flexible N‐termini and loop regions differed within the half‐capsids and at the waist, explaining partly the unusual twin structure. Basic amino acid residues inside the capsid form a positively charged pocket next to the five‐fold axis of the capsomer suitable to bind DNA. Within this pocket, density most likely corresponding to DNA was resolved