Distinct Structural Dynamics of the Semiquinone State Define a Signalling Pathway in Avian Cryptochrome

The light-dependent magnetic compass of night-migratory songbirds is widely hypothesized to rely on the radical pair mechanism within retinal cryptochrome. However, bridging the mechanistic gap between microsecond quantum spin dynamics and the long-lived, global protein conformational changes required for cellular signalling remains a formidable challenge. Here, we apply redox state-resolved hydrogen/deuterium-exchange mass spectrometry (HDX-MS) to map the conformational landscape of European robin cryptochrome 4a (ErCry4a) across its photocycle. We reveal that photochemical reduction drives robust, allosteric structural transitions across key functional nodes, including the phosphate-binding loop (PBL), protrusion loop (PL), FAD-proximal helix {\alpha}17, and the C-terminal {\alpha}22/{\alpha}23 network. Crucially, we isolate the structural fingerprint of the transient semiquinone, the presumed signalling species. Rather than acting as a linear structural stepping-stone, the semiquinone exhibits a distinct, non-monotonic conformational signature characterized by a transient destabilization of the PBL and PL, contrasting sharply with the global rigidification observed in the fully reduced state. These findings establish the semiquinone as a structurally unique and functionally competent biological entity. Our results provide direct biophysical evidence for a dedicated, high-fidelity structural signalling cascade, detailing how localized quantum-level photochemistry is translated into the precise conformational dynamics required for animal navigation.