The light-harvesting chlorophyll (Chl) a/b binding protein of photosystem II (LHCIIb) fulfils multiple functions, such as light harvesting and energy dissipation under different illuminations. The crystal structure of LHCIIb at the near atomic resolution reveals an anti-parallel strands structure in the lumenal loop between the transmembrane (TM) helices B/C. In order to study the structural and functional significances of this structure, three amino acids (V119, H120 and S123) in this region have been exchanged to F, L and G, respectively, and the influence of the mutagenesis on the structure and function of LHCIIb has been investigated. The results are as follows: 1) Circular dichroism (CD) spectra of the mutations reveals that the anti-parallel strands in the lumenal region are very important for adjusting pigment conformation in the neoxanthin (Neo) domain of LHCIIb. Although the mutagenesis causes only a slight loss of the Neo binding in the complexes (V119F, 0.09; S123G, 0.19; and H120L, 0.27), it imparts remarkable changes to the pigment conformation. 2) Substituting S123 with G results in a higher susceptibility to photo-damage, an increased tendency to aggregate, and enhanced fluorescence quenching induced by the medium acidification. These results demonstrate that this anti-parallel strands domain plays an important role in regulating the pigment conformation and in adjusting the aggregation and the fluorescence yield of LHCIIb.