The collisions of noble gas atoms with graphene and a graphene nanodome were investigated by employing first principles molecular dynamics calculations. By analyzing the electron-related properties of the collision process, the atom dynamics and the deformation of the graphene/nanodome, our results show a difference between the elastic properties of the nanodome and graphene. Generally, the nanodome can more easily revert to its initial conformation. The final kinetic energy, E_f, of the atom that collides with the nanodome is larger than the E_f of the atom that collides with graphene. In addition, the relationship between the initial kinetic energy of the atom, E_k0, and its corresponding proportion of energy loss, χ, is linear (except for the Kr atom). Our research will probably contribute to the investigation of the 2D materials' mechanical properties and their surface morphology. Moreover, due to its novel mechanical properties, the graphene nanodome is an extraordinary nano-architecture which can be employed to protect nano-devices from damage and injury.