A Structural Landscape of Fungal Allergens with Epitope-Level Resolution Reveals Cross-Kingdom Structural Similarity

The immunological properties of allergens are ultimately governed by three-dimensional protein structure, particularly the spatial organization of IgE-binding epitopes. Despite the need to capture global structural relationships and patterns of allergen diversity, most allergen classification and prediction strategies still rely predominantly on sequence-based approaches. Here, we present a structure-based framework that represents fungal allergens as elements embedded within a continuous structural manifold. Using AlphaFold-predicted full-length structures of 150 previously reported fungal allergens, we constructed a global structural distance space defined by TM-score-derived similarities. This manifold revealed a heterogeneous yet continuous landscape in which dense structural neighborhoods correspond to established allergen families, while more diffuse regions reflect gradual structural transitions. To directly link global protein architecture with immunologically relevant features, we extended this framework to epitope-level structural representations derived from predicted antibody-binding regions. Epitope-restricted structures preserved the relative organization of major allergen clusters, demonstrating that IgE-relevant features are embedded within conserved structural scaffolds. At the same time, epitope-level analysis demonstrated that high structural similarity can be observed at the epitope level even when global protein folds differ, highlighting the contribution of local structural features to immunologically relevant properties. We further applied a nearest-neighbor-based manifold inclusion analysis to screen nearly 20,000 fungal protein structures, identifying numerous allergen-related proteins occupying the same structural neighborhoods as known allergens, thereby extending allergen-associated architectures beyond current databases. Finally, structural screening of non-fungal allergens revealed cross-kingdom similarities to fungal allergens, suggesting convergent allergenic architectures across distant taxa. Together, this study establishes a unified structural manifold framework that integrates full-length protein and epitope-level information, providing a structure-based perspective on allergen diversity as a continuous space and on cross-reactivity.