Octahedral molecular sieves (OMS) attract increasing interest in the search for novel electrode materials for energy storage and water desalination. While a nanometric particle size is desirable for such applications, this makes ordinary single-crystal characterization difficult and many OMS structures are still waiting for elucidation. Here we present the long awaited structure of a well known material, (Na,□)5[MnO2]13, resolved by a combination of electron diffraction tomography, dynamical scattering theory and X-ray powder Rietveld refinement. A new type of tunnel structure was found, able to explain previously reported electrochemical properties. This structure also suggests a possible mechanism for topotactic transformations between different manganese oxide OMS frameworks.