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A C-type lectin (CfLec-3) from Chlamys farreri with three carbohydrate-recognition domains (CRDs) was selected to dissect the possible mechanisms of PAMP binding and functional differentiation of invertebrate lectins. CfLec-3 distributed broadly, and its mRNA expression in hemocytes increased significantly after stimulations with LPS, PGN or β-glucan, but not poly(I:C). The recombinant CfLec-3 (rCfLec-3) could bind PAMPs and several microbes. rCfLec-3 mediated hemocytes phagocytosis against Escherichia coli and encapsulation towards agarose beads. Obvious functional differentiation occurred among the three CRDs, as CRD1 exhibited higher activity to bind PAMPs, while CRD2/3 were expert in promoting hemocyte mediated opsonisation. The tertiary structural differences were suspected to be associated with such functional differentiation. PAMP binding abilities of CfLec-3 were determined by Ca2+-binding site 2 motif. When Pro in this motif of each CRD was mutated into Ser, their PAMP binding abilities were deprived absolutely. rCRD2 acquired mannan binding capability when its EPD was replaced by EPN, but lost when EPN in rCRD3 was changed into EPD. The Pro in Ca2+-binding site 2 was indispensable for PAMPs binding, while Asn was determinant for specific binding to mannan. It shed new insight into PAMPs binding mechanism of invertebrate C-type lectins and their functional differentiation. [ABSTRACT FROM AUTHOR]