We report the successful fabrication of optically active three-dimensional (3D) superlattices that incorporate DNA-encoded components, metallic nanoparticles, and molecular chromophores in well-defined positions. A DNA linker with three distinct binding sites serves as an assembly agent and dynamically tunable structural element for the superlattice. Using small angle X-ray scattering we have revealed the organization of particle-chromophore 3D arrays and monitored their reversible contractions and expansions that were modulated by ionic strength changes. As the distance between the molecular chromophores and plasmonic nanoparticles in the superlattice was regulated in situ, we were able to uncover the relationship between experimentally determined structure and optical response of the system. This dynamical tunability of superlattice results in a dramatic optical response: nearly a three times change of emission rate of the chromophore. The evolution of lifetime with structural changes reasonably agrees with the calculations based on a cumulitative coupling of chromophores with metallic nanoparticles in different coordination shells.