• Genome mining identified a novel 'mini-N type' subclass of MgtE channels lacking canonical N and CBS domains.
• Mini-N-type MgtE homologs were unstable and could not be purified using standard methods.
• De novo-designed proteins were created and their crystal structures determined, enabling fusion to mini-N-type MgtE.
• Fusion with a de novo protein facilitated successful purification and preliminary cryo-EM imaging of mini-N-type MgtE.