A Two-Component Pseudo-Icosahedral Protein Nanocompartment with Variable Shell Composition and Irregular Tiling

Protein shells or capsids are a widespread form of compartmentalization in nature. Viruses use protein capsids to protect and transport their genomes while many cellular organisms use protein shells for varied metabolic purposes. These protein-based compartments often exhibit icosahedral symmetry and consist of a small number of structural components with defined roles. Encapsulins are a prevalent protein-based compartmentalization strategy in prokaryotes. All encapsulins studied thus far consist of a single shell protein that adopts the viral Hong Kong 97 (HK97)-fold. Here, the characterization of a Family 2B two-component encapsulin from Streptomyces lydicus is reported. The differential assembly behavior of the two shell components and their ability to co-assemble into mixed shells with variable shell composition is demonstrated. The structures of both shell proteins are determined using cryo-electron microscopy. Using 3D-classification and cross-linking studies, the irregular tiling of mixed shells is highlighted. This work expands the known assembly modes of HK97-fold proteins and lays the foundation for future functional and engineering studies on two-component encapsulins.