The chaperonin GroEL interacts with various proteins, leading them to adopt their correct conformations with the aid of GroES and ATP. The actual mechanism is still being debated. In this study, by use of cryo-electron microscopy, we determined the solution structure of the Thermus thermophilus GroEL-GroES complex encapsulating its substrate proteins. We observed the averaged density of substrate proteins in the center of the GroEL-GroES cavity. The position of the averaged substrate density in the cavity suggested a repulsive interaction between a majority of the substrate proteins and the interior wall of the cavity, which is suitable for substrate release. In addition, we observed a distortion of the cis-GroEL ring, especially at the position near the substrate, which indicated that the interaction between the encapsulated proteins and the GroEL ring results in an adjustment in the cavity's shape to accommodate the substrate.