Intermolecular and intramolecular interactions of the extrinsic 33-kDa protein in photosystem II were investigated by cross-linking with a water-soluble carbodiimide as cross-linking agent. This zero-length cross-linker is known to cross-link the 33-kDa protein to the chlorophyll-alpha-binding protein CP47 [Bricker, T M., Odom, W. R. & Queirolo, C. B. (1988) FEBS Lett. 231, 111-117; Enami, I., Kaneko, M., Kitamura, N., Koike, H., Sonoike, K., Inoue, Y. & Katoh, S. (1991) Biochim. Biophys. Acta 1060, 224-232]. In this work, cross-linking was observed not only to CP47 but also to a small intrinsic subunit. In addition, through the use of a high-resolution SDS-gel system, three intramolecular cross-linked products of the 33-kDa protein were detected. To search for additional cross-linking sites that might not be accessible to the cross-linker in intact photosystem II, the isolated 33-kDa protein was activated for cross-linking and subsequently bound to CaCl2-washed photosystem II. In the complementary experiment, CaCl2-washed photosystem II was activated, then reconstituted with the 33-kDa protein. The results of the crosslinking reactions demonstrated that all carboxylic acid groups involved in cross-linking were located on the 33-kDa protein and all primary amines were located on intrinsic membrane proteins. No cross-linking other than those observed in cross-linking experiments with intact photosystem II were observed. This indicated that the 33-kDa protein is bound to CP47 and a small subunit but not to the photosystem II reaction centre. This observation is consistent with the finding that cross-linking was independent of the presence or absence of the manganese cluster. Possible residues on the 33-kDa protein and CP47 involved in cross-linking are suggested.