3D structural determination of biological macromolecules is not only critical to understanding their mechanisms, but also essential in structural based drug discovery. Combining the high resolution imaging of TEM and efficient computer processing, protein structures in solution or in 2D crystals can be determined. Using lipid monolayer technique with Ni-NTA modified lipid, which has high affinity to 6His-tagged proteins, 2D crystal of the protein can be formed at the lipid surface. In this study, several proteins have been crystallized using this technique, including the SARS virus Nsp15 endonuclease and the human Toll-like receptor 3 extracellular domain. This approach may also have application in nanofabrication, taking advantage of the natural building bloc of proteins and virus. Single particle analysis can determine protein structures in solution without the need for crystals. 3D structures of several protein complexes had been solved by the single particle method, including IniA from Mycobacterium tuberculosis, Nsp15 and TLR3 ECD. Determining the structures of these proteins is an important step toward understanding pathogenic microbes and our immune system.