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Here we propose an E(3)-equivariant deep-learning framework to represent density functional theory (DFT) Hamiltonian as a function of material structure, which can naturally preserve the Euclidean symmetry even in the presence of spin-orbit coupling. Our DeepH-E3 method enables very efficient electronic-structure calculation at ab initio accuracy by learning from DFT data of small-sized structures, making routine study of large-scale supercells ($> 10^4$ atoms) feasible. Remarkably, the method can reach sub-meV prediction accuracy at high training efficiency, showing state-of-the-art performance in our experiments. 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