This paper addresses the question of whether the PsbS protein of photosyste
m two (PS II) is located within the LHC II-PS II supercomplex for which a t
hree-dimensional structure has been obtained by cryoelectron microscopy and
single particle analysis. The PsbS protein has recently been implicated as
the site for non-photochemical quenching. Based both on immunoblotting ana
lyses and structural considerations of an improved model of the spinach LHC
II-PS II supercomplex, we conclude that the PsbS protein is not located wi
thin the supercomplex. Analyses of other fractions resulting from the solub
ilization of PS II-enriched membranes derived from spinach suggest that the
PsbS protein is located in the LHC II-rich regions that interconnect the s
upercomplex within the membrane.