Limited studies have been done on the interactions between subunits of self-assembling protein cages. E2 protein cage from Bacillus stearothermophilus was investigated in this work to impart pH sensitive disassembly profile. Key amino acids were identified at the intratrimer and intertrimer interfaces, and histidine residues were introduced to these key sites to probe for their influences on the E2 assembly. We found that both the intratrimer- and the intertrimer-modified mutant proteins have the same quaternary structures as the wild type (E2-WT) at physiological pH of 7.4. At pH 5.0, the intratrimer-modified protein maintained its spherical structure. In contrast, the intertrimer modified protein lost its integrity, as observed under the electron microscope, whereas it remained soluble and nondenatured. The identified interactions between the intertrimers are critical in the formation of E2 protein cage. The pH-controlled disassembly of E2 protein cage in soluble and nondenatured form make it promising in nanoscale applications, especially for drug delivery and release in the endosomes.