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Significance Grapevine fanleaf virus (GFLV), a picorna-like plant virus, severely affects vineyards worldwide. While nanobodies (Nbs) confer resistance to GFLV in plants, the underlying molecular mechanism of action is unknown. Here we present the high-resolution cryo electron microscopy structure of the GFLV–Nb complex. It uncovers the epitope on the capsid surface, which is a composite binding site into which the antigen loop is accommodated through an induced fit mechanism. Furthermore, we describe several resistance-breaking isolates of GFLV with reduced Nb binding capacity. Those escape variants that carry a C-terminal extension in the capsid protein also fail to be transmitted by nematodes. Together, these data provide structure–function insights into Nb–GFLV recognition and the molecular mechanism leading to loss of resistance.

Structural basis of nanobody recognition of grapevine fanleaf virus and of virus resistance loss