Photosystem II (PSII), a large pigment protein complex, undergoes rapid turnover under natural conditions. During assembly of PSII, oxidative damage to vulnerable assembly intermediate complexes must be prevented. Psb28, the only cytoplasmic extrinsic protein in PSII, protects the RC47 assembly intermediate of PSII and assists its efficient conversion into functional PSII. Its role is particularly important under stress conditions when PSII damage occurs frequently. Psb28 is not found, however, in any PSII crystal structure, and its structural location has remained unknown. In this study, we used chemical cross-linking combined with mass spectrometry to capture the transient interaction of Psb28 with PSII. We detected three cross-links between Psb28 and the α-and β-subunits of cytochrome b 559 , an essential component of the PSII reaction-center complex. These distance restraints enable us to position Psb28 on the cytosolic surface of PSII directly above cytochrome b 559 , in close proximity to the Q B site. Protein-protein docking results also support Psb28 binding in this region. Determination of the Psb28 binding site and other biochemical evidence allow us to propose a mechanism by which Psb28 exerts its protective effect on the RC47 intermediate. This study also shows that isotope-encoded cross-linking with the "mass tags" selection criteria allows confident identification of more cross-linked peptides in PSII than has been previously reported. This approach thus holds promise to identify other transient proteinprotein interactions in membrane protein complexes.is a multisubunit pigment-protein complex embedded in the thylakoid membranes of cyanobacteria, algae, and plants. PSII uses light energy to oxidize water to molecular oxygen, simultaneously reducing plastoquinone. Active PSII consists of ∼20 protein subunits and multiple light-harvesting and redox-active cofactors (1, 2).As a result of demanding electron-transfer chemistry, PSII undergoes frequent oxidative damage, necessitating a complex cycle of repair and reassembly (reviewed in ref.3). The assembly occurs stepwise via multiple transient intermediate complexes that are difficult to study because of their low abundance, relatively short lifetimes, and heterogeneity. Crystal structures of the active complex from thermophilic cyanobacteria are available (1, 4, 5), but they do not capture the transient interactions of the various accessory proteins that regulate the life cycle by binding exclusively to intermediate subcomplexes. Nevertheless, significant progress has been made in characterizing these intermediates through complementary use of genetic modification, biochemical analysis, and mass spectrometry (MS) (3, 6-9). Although crystal structures of assembly intermediate complexes are not available, the binding site of one accessory protein, Psb27, on the luminal surface of PSII has been determined by chemical cross-linking and MS (10, 11). This knowledge complements functional studies of Psb27 and provides mechanistic insight into how Psb27 prote...