The structure determination of membrane protein in lipid environment can be carried out using cryo-electron microscopy combined with the recent development of data collection and image processing. We describe a protocol to study assemblies or stacks of membrane protein reconstituted into a lipid membrane using both cryo-electron tomography and single particle analysis, which is an alternative approach to electron crystallography for solving 3D structure. We show the organization of the successive layers of OprM molecules revealing the protein-protein interactions between OprM molecules of two successive lipid bilayers.