To analyze the PSII structure in more detail, we have obtained the crystal structure of PSII from another thermophilic cyanobacterium, Thermosynechococcus vulcanus, at 3.7-Å resolution. The present structure was built on the basis of the sequences of PSII large subunits D1, D2, CP47, and CP43; extrinsic 33-and 12-kDa proteins and cytochrome c550; and several low molecular mass subunits, among which the structure of the 12-kDa protein was not reported previously. This yielded much information concerning the molecular interactions within this large protein complex. We also show the arrangement of chlorophylls and cofactors, including two -carotenes recently identified in a region close to the reaction center, which provided important clues to the secondary electron transfer pathways around the reaction center. Furthermore, possible ligands for the Mn-cluster were determined. In particular, the C terminus of D1 polypeptide was shown to be connected to the Mn cluster directly. The structural information obtained here provides important insights into the mechanism of PSII reactions.T he photosystem II (PSII) complex is a multisubunit membrane-protein complex consisting of Ͼ14 membranespanning subunits, 3 hydrophilic peripheral subunits, and Ͼ40 cofactors, including chlorophylls (chls), carotenoids, Mn, Fe, and plastoquinones, with a total molecular mass of 320 kDa for a monomer (for review, see refs. 1-3). The PSII reaction center (RC) P680 is a (pair of) chl a coordinated by RC D1- and undergoes charge separation on absorption of light energy; the electrons thus generated are transferred to pheophytin, the first quinone acceptor Q A , and then the second quinone acceptor Q B . At the oxidizing side of PSII, a redoxactive tyrosine residue D1-Tyr-161 (Tyr Z ) reduces P680. The oxidized Tyr Z withdraws electrons from a Mn cluster consisting of four Mn atoms, which in turn withdraws electrons in a sequential way from water molecules, leading to the splitting of water and formation of molecular oxygen. This reaction provides us with the oxygen-rich atmospheric environment suitable for most of the organisms to live on the earth, whereas the protons yielded are the source for proton gradient across the thylakoid membrane required for ATP formation.In view of its importance, PSII has received extensive studies in the past several decades regarding its protein composition, function, and dynamic regulation. As a result, our understanding of the function and reaction mechanisms of PSII has increased greatly. However, studies of the structure of PSII have appeared only in recent years. The 3D image of PSII was first studied by electron cryomicroscopy of 2D crystals of various PSII particles, and a structure at 8-Å resolution has been reported for a CP47-RC-PSII complex, which lacked oxygen-evolving activity, and its related three extrinsic proteins (4, 5). Recently, 3D crystals have been obtained for oxygen-evolving PSII complexes from two species of thermophilic cyanobacteria (6-8), and the PSII crystal structure from one of...