Protein cross-linking and radiolytic footprinting coupled with highresolution mass spectrometry were used to examine the structure of PsbP and PsbQ when they are bound to Photosystem II. In its bound state, the N-terminal 15-amino-acid residue domain of PsbP, which is unresolved in current crystal structures, interacts with domains in the C terminus of the protein. These interactions may serve to stabilize the structure of the N terminus and may facilitate PsbP binding and function. These interactions place strong structural constraints on the organization of PsbP when associated with the Photosystem II complex. Additionally, amino acid residues in the structurally unresolved loop 3A domain of PsbP ( 90 K-107 V), 93 Y and 96 K, are in close proximity (≤11.4 Å) to the N-terminal 1 E residue of PsbQ. These findings are the first, to our knowledge, to identify a putative region of interaction between these two components. Cross-linked domains within PsbQ were also identified, indicating that two PsbQ molecules can interact in higher plants in a manner similar to that observed by Liu et al. [(2014) Proc Natl Acad Sci 111 (12):4638-4643] in cyanobacterial Photosystem II. This interaction is consistent with either intra-Photosystem II dimer or inter-Photosystem II dimer models in higher plants. Finally, OH • produced by synchrotron radiolysis of water was used to oxidatively modify surface residues on PsbP and PsbQ. Domains on the surface of both protein subunits were resistant to modification, indicating that they were shielded from water and appear to define buried regions that are in contact with other Photosystem II components.oxidoreductase that is found in all oxygenic photosynthetic organisms. This membrane protein complex contains at least 20 protein subunits, 17 of which are intrinsic membrane proteins. Higher plants contain three extrinsic proteins associated with the complex-PsbO, PsbP, and PsbQ-whereas cyanobacteria contain PsbO, PsbU, PsbV, and CyanoQ (a homolog of PsbQ). In higher plants the PsbO, PsbP, and PsbQ proteins are required for optimal rates of O 2 evolution under physiological inorganic calcium and chloride concentrations (1, 2).The PsbO protein appears to play a central role in the stabilization of the manganese cluster in all oxygenic photosynthetic organisms (3). In higher plants, PsbO and PsbP are required for photoautotrophic growth, PS II assembly, and the stabilization of PS II supercomplexes (4-9), with PsbP also being required for normal thylakoid assembly (6). Under low-light growth conditions, PsbQ is required for photoautotrophy (10).Although the crystal structure of cyanobacterial PS II has been resolved to 1.9 Å (11), no crystal structures for higher plant PS II have been presented. The structure and interactions of PsbO with the intrinsic subunits have been approximated by analogy to the cyanobacterial photosystem. Although high-resolution crystal structures of isolated spinach PsbP [1.98 Å; Protein Data Bank (PDB) ID code 2VU4] (12) and PsbQ (1.49 Å; PDB ID code 1VYK) are avai...