Inorganic ions may direct the self-assembly of biomacromolecules into nanostructures which can further be used as a reactant and matrix for nanomaterials synthesis and assembly. Here we use bone mineral and filamentous bacteriophage as a model to demonstrate this concept. Divalent calcium ions are found to trigger the electrostatic self-assembly of anionic nanofiber-like bacteriophages into bundle structures where calcium ions are pre-organized between bacteriophage nanofibers. The resultant Ca(2+)-bacteriophage bundles can be separated and purified from the aqueous solution. The nanostructures of the bundles are verified by zeta potential analysis, small angle x-ray scattering and transmission electron microscopy. Because of the transcription of the bacteriophage chiral surface to the periodic alignment of pre-loaded Ca(2+), the Ca(2+)-bacteriphage bundles can serve as both Ca sources and biotemplates to initiate the oriented nucleation and growth of nanocrystalline hydroxyapatite in phosphate solution or in simulated body fluid. This work provides new insights into biomineralization and represents a new approach to the fabrication of biomolecular-inorganic hybrid layered nanostructures.