Over the last 9 years, the structures of the various components of the bacterial photosynthetic apparatus or their homologues have been determined by x-ray crystallography to at least 4.8-Å resolution. Despite this wealth of structural information on the individual proteins, there remains an urgent need to examine the architecture of the photosynthetic apparatus in intact photosynthetic membranes. Information on the arrangement of the different complexes in a native system will help us to understand the processes that ensure the remarkably high quantum efficiency of the system. In this work we report images obtained with an atomic force microscope of native photosynthetic membranes from the bacterium Rhodospirillum photometricum. Several proteins can be seen and identified at molecular resolution, allowing the analysis and modeling of the lateral organization of multiple components of the photosynthetic apparatus within a native membrane. Analysis of the distribution of the complexes shows that their arrangement is far from random, with significant clustering both of antenna complexes and core complexes. The functional significance of the observed distribution is discussed. I n photosynthesis, highly efficient multiprotein assemblies convert sunlight into chemical potential energy. This process requires several different membrane proteins that funnel light energy to the primary reaction center (RC) and then ensure a cyclic electron transfer chain that converts this energy into an electrochemical potential (1) and, finally, an ATP synthase that is able to store the energy in the phosphodiester bond of ATP (2). A challenge in structural biology is to analyze the structural basis of this efficiency in native membranes. More precisely, the relationship between the different components of the system that ensure efficient energy and electron transfer needs to be determined (3, 4).In photosynthetic bacteria, a large amount of structural information about the individual components of the photosynthetic unit (PSU) is available. The PSU is an assembly made up of the RC associated with the light-harvesting proteins LH1 and LH2, containing chlorophylls and carotenoids. All components cooperate in absorbing light effectively and channeling energy to the RC. In particular, high-resolution structures of two LH2s from Rhodopseudomonas acidophila and Rhodospirillum molischianum and of two RCs from Rhodopseudomonas viridis and Rhodobacter sphaeroides are available (5-9). Electron crystallography data have revealed a hexadecameric assembly of LH1 around the RC in Rhodospirillum rubrum (10, 11). More recently, atomic force microscope (AFM) topographs of native membranes of R. viridis could be acquired. The data unambiguously reported an elliptical hexadecameric arrangement of the LH1 around each RC in a noncrystalline native environment (12). A 4.8-Å x-ray structure of the core complex of Rhodopseudomonas palustris was also elliptical, but with 15 LH1 subunits and one unidentifiable peptide subunit surrounding the RC (13). This str...