Self-organized large-scale flow structures occur in a wide range of turbulent flows. Yet, their emergence, dynamics, and interplay with small-scale turbulence are not well understood. Here, we investigate such self-organized turbulent superstructures in three-dimensional turbulent Kolmogorov flow with large-scale drag. Through extensive simulations, we uncover their low-dimensional dynamics featuring transitions between several stable and meta-stable large-scale structures as a function of the damping parameter. The main dissipation mechanism for the turbulent superstructures is the generation of small-scale turbulence, whose local structure depends strongly on the large-scale flow. Our results elucidate the generic emergence and low-dimensional dynamics of large-scale flow structures in fully developed turbulence and reveal a strong coupling of large-and small-scale flow features.