Artificial protein assemblies require a method to conjugate two or more proteins in a stable and predictable structure. “Shared helix method” is useful for protein engineering that fuses the exposed alpha helices from two different protein components rigidly and predictably. In this study, the successful design of these novel fusion proteins, Putrescine aminotransferase (YgjG) complexes, was confirmed by X-ray crystallography. Also, we applied shared helix method to structural analysis of small target proteins (~<100kDa) using cryo-EM. To overcome size limitations in cryo-EM, we selected glutamate dehydrogenase (GDH) as a scaffold protein to determine the structure of small target proteins and the protein assemblies were successfully constructed using shared helix method. This application does not need to optimize the extra sequence of linker to connect each protein and forms stable complex conformation. Since, using the high molecule protein and small target protein complex, which was fused by alpha helix fusion method, is capable to assemble the cryo-EM and may improve to be convenient tool for cryo-EM analysis of small target protein.