Properties of the organic matrix of bone1 as well as its function in the microstructure2 could be the key to the remarkable mechanical properties of bone3. Previously, it was found that on the molecular level, calcium-mediated sacrificial bonds increased stiffness and enhanced energy dissipation in bone constituent molecules4,5. Here we present evidence for how this sacrificial bond and hidden length mechanism contributes to the mechanical properties of the bone composite, by investigating the nanoscale arrangement of the bone constituents6–8 and their interactions. We find evidence that bone consists of mineralized collagen fibrils and a non-fibrillar organic matrix2, which acts as a ‘glue’ that holds the mineralized fibrils together. We believe that this glue may resist the separation of mineralized collagen fibrils. As in the case of the sacrificial bonds in single molecules5, the effectiveness of this mechanism increases with the presence of Ca2+ ions.