In photosynthesis, highly organized multiprotein assemblies convert sunlight into biochemical energy with high efficiency. A challenge in structural biology is to analyze such supramolecular complexes in native membranes. Atomic force microscopy (AFM) with high lateral resolution, high signal-to-noise ratio, and the possibility to nanodissect biological samples is a unique tool to investigate multiprotein complexes at molecular resolution in situ.Here we present high-resolution AFM of the photosynthetic core complex in native Rhodopseudomonas viridis membranes. Topographs at 10-Å lateral and Ϸ1-Å vertical resolution reveal a single reaction center (RC) surrounded by a closed ellipsoid of 16 lightharvesting (LH1) subunits. Nanodissection of the tetraheme cytochrome (4Hcyt) subunit from the RC allows demonstration that the L and M subunits exhibit an asymmetric topography intimately associated to the LH1 subunits located at the short ellipsis axis. This architecture implies a distance distribution between the antenna and the RC compared with a centered location of the RC within a circular LH1, which may influence the energy transfer within the core complex. The LH1 subunits rearrange into a circle after removal of the RC from the core complex. P hotosynthetic organisms fuel their metabolism with light energy and have developed for this purpose an efficient apparatus for harvesting and converting sunlight into biochemical energy. The initial steps of photosynthesis, universal in photosynthetic bacteria, algae, and higher plants, comprise light absorption by a set of light-harvesting (LH) pigment-protein complexes and subsequent transfer of the excitation energy to the reaction center (RC), where charge separation across the membrane takes place. In photosynthetic bacteria, the so-called core complex, constituted of a RC intimately associated with LH1, performs these initial steps of the photosynthesis: light trapping and charge separation. The efficiency of the process demands high structural organization of the components. The spatial organization between LH1 and RC is still a matter of debate (1-8), and no information on their assembly in a native system is available. Complementary to structure determination of individual components at near-atomic resolution (9-11), one of the main challenges today is to describe the supramolecular organization of the photosynthetic machinery in native membranes (12). From a more general standpoint, structural biology is in need of a technique with a lateral resolution and signalto-noise ratio good enough to identify individual components of a multiprotein complex in situ (13).The atomic force microscope (14) has developed into a powerful tool in structural biology (15,16). It was demonstrated that topographs of two-dimensional crystals of membrane proteins can be acquired at subnanometer resolution (17). In addition, the high signal-to-noise ratio in raw data atomic force microscopy (AFM) topographs allows single-molecule imaging (16,18,19). Furthermore, by applying loading forc...