The AP205 VLP can be aggregated with the polycation pMETAC into 3D hexagonal closedpacked superstructures. The liquid crystal structure of the suprastructure is controlled by the pH of the solution, the ionic strength, and the surface chemistry of the protein nanocages. The roughness of the protein nanocage and the directionality of interaction forces play a role in selfassembly. This work showcases the effect of surface roughness and directional interaction between the biological-derived building blocks, which, to our knowledge, has been shown in simulations or simplified Janur particles yet. The findings of this work give a new perspective to the ongoing discussion in the literature on whether the RNA affects the apparent surface charge or the hydrophobicity of the nanocages. This, in turn, provides insight into how the cargo loading influences nanocage selfassembly and interactions with the surroundings, which is crucial for crossing biological barriers.