Although the structural basis for how BMAL1/CLOCK interact with the E-box is unknown, recent research has shown that the bHLH protein domains of BMAL1/CLOCK are highly similar to other bHLH containing proteins, e.g. Myc/Max, which have been crystallized with E-boxes.
The underlying mechanism for how BMAL1/CLOCK interacts with the E-box remains unexplored. However, recent research has demonstrated that the bHLH protein domains of BMAL1/CLOCK share considerable homology with those found in Myc/Max proteins, which have been structurally characterized in complex with E-boxes.