Root-specific cadmium (Cd) transporter that mediates Cd efflux in root vacuoles. Involved in Cd detoxification by sequestrating Cd into root vacuoles and limiting translocation of Cd from the roots to the shoots, and accumulation in grains. ATP + H2O + Zn(2+)(in) = ADP + H(+) + phosphate + Zn(2+)(out) ATP + Cd(2+)(in) + H2O = ADP + Cd(2+)(out) + H(+) + phosphate Localizes to the tonoplast of root cells. Specifically expressed in roots. A single amino acid substitution of Arg-80 to His abolishes HMA3 cadmium transport activity through the tonoplast in root cells. This allele is found in a number of rice cultivars, and is associated with high accumulation of cadmium in rice grains. Identification of natural allelic variation in HMA3 may facilitate the development of rice varieties with grain cadmium concentrations adapted to dietary needs in function of the cadmium concentration in soil. Over-expression of HMA3 allows to reduce efficiently cadmium accumulation in the grain and to enhance cadmium tolerance in rice. Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IB subfamily.