Based on an improved isolation procedure using perfusion chromatography, trimeric Photosystem 1 (PS1) complexes have been isolated from various deletion mutants of the mesophilic cyanobacterium Synechocystis PCC 6803. These mutants are only deficient in the deleted subunits, which was carefully checked by high resolution gel electrophoresis in combination with immunoblotting. These highly purified and well characterized PS1 particles were then examined by electron microscopy, followed by computer-aided image processing with single particle averaging techniques as described earlier (Kruip, J., Boekema, E. J., Bald, D., Boonstra, A. Photosystem 1 (PS1) 1 is one of the two transmembrane pigment-protein complexes of oxygenic photosynthesis located in the thylakoid membrane of chloroplasts and cyanobacteria. Its main function is the light-dependent electron transfer from plastocyanin (or cytochrome c 6 ) on the lumen side to soluble ferredoxin (or flavodoxin) on the cytoplasmic or stroma side, thereby transforming light energy into reducing power for various biosynthetic pathways (see Refs. 1-3 for reviews). Cyanobacterial PS1 consists of 11 subunits, named PsaA to PsaM, with PsaG and PsaH missing, as they are found only in chloroplasts (3); all their sequences are known (1). The hydrophilic subunits PsaC, -D, and -E are localized on the cytoplasmic side (4), and PsaF is supposed to sit on the lumenal side of the thylakoid membrane. All the other subunits are integral membrane proteins.In terms of function the initial steps of light harvesting and charge separation are carried out by only three proteins. The PsaA/PsaB heterodimer harbors the primary electron donor P700 (a chlorophyll dimer) and the electron acceptors A 0 (a monomeric chlorophyll), A 1 (a phylloquinone), and F X (a [4Fe4S] iron-sulfur cluster) in addition to about 100 -130 antenna chlorophyll molecules (5). PsaC contains the terminal electron acceptors F A and F B (both [4Fe4S] iron-sulfur clusters). The other proteins do not bind any cofactors, but fulfill important functional and structural roles: PsaD and -F have been shown to be candidates for ferredoxin (6, 7) and plastocyanin docking (8, 9), respectively. PsaE plays an important role in cyclic electron flow (10) and ferredoxin reduction (11,12), while PsaL and PsaD are important for trimer formation (4,13,14).To elucidate the function of all subunits on a molecular level, a high resolution structure is necessary. Despite several crystallization reports (15-17), a low-resolution x-ray analysis (6 Å) for PS1 from the thermophilic cyanobacterium Synechococcus elongatus became available only in 1993 (18). Recently this x-ray analysis was extended to 4 Å (19, 57). In this study, 31 transmembrane, 9 surface, and 3 stromal ␣-helices, 65 chlorophyll a molecules, and three [4Fe4S] clusters could be fitted into the electron density map. Due to the medium resolution it is not possible to attribute the identified structural elements * The costs of publication of this article were defrayed in part by the pay...