The discovery of perfectly ordered 3D mesoporous protein/silica structure in the axial filament of the marine sponge Monorhaphis chuni is reported. The structure belongs to body-centered tetragonal symmetry system (a = 9.88 nm, c = 10.83 nm) and comprises interconnecting lattices of protein and silica, templated by the self-assembled, enzymatically active protein-silicatein, whose primary function is the precipitation of silica.