Protein-DNA recognition is fundamental to biological processes. This review revises the understanding of protein-DNA interactions, emphasizing the three-dimensional structures of both macromolecules. Protein-DNA interactions are divided into base readout (recognizing DNA base chemical signatures) and shape readout (recognizing DNA shape). Base readout occurs in major or minor grooves, while shape readout includes global (e.g., DNA bending) and local (e.g., DNA kinks) variations. Over 1500 protein-DNA structures show that DNA-binding proteins use multiple readout mechanisms for specificity. Base readout in the major groove distinguishes between protein families, while shape readout provides higher resolution specificity within families. DNA shape is influenced by sequence-dependent structural variations, such as DNA bending, A-DNA, Z-DNA, and minor groove narrowing. These structural variations are recognized by proteins, contributing to binding specificity. DNA shape also affects electrostatic potentials, which proteins can read. Proteins use both direct (base-specific hydrogen bonds) and indirect (shape-dependent) readout mechanisms. The review proposes replacing "direct" and "indirect" readout with "base" and "shape" readout, reflecting how proteins recognize DNA sequences. DNA-binding proteins use a range of structural motifs, including helix-turn-helix, winged helix-turn-helix, helix-loop-helix, and beta-sandwich domains. These motifs interact with DNA in the major or minor groove, using hydrogen bonds, hydrophobic contacts, or shape recognition. DNA structure varies sequence-dependent, with B-DNA, A-DNA, Z-DNA, and other conformations. These variations are recognized by proteins, contributing to specificity. DNA bending, kinks, and minor groove narrowing are also recognized by proteins. The review highlights the complexity of protein-DNA recognition, involving multiple readout mechanisms and structural variations in DNA. Understanding these mechanisms is essential for accurately annotating genome sequences and understanding DNA-protein interactions.Protein-DNA recognition is fundamental to biological processes. This review revises the understanding of protein-DNA interactions, emphasizing the three-dimensional structures of both macromolecules. Protein-DNA interactions are divided into base readout (recognizing DNA base chemical signatures) and shape readout (recognizing DNA shape). Base readout occurs in major or minor grooves, while shape readout includes global (e.g., DNA bending) and local (e.g., DNA kinks) variations. Over 1500 protein-DNA structures show that DNA-binding proteins use multiple readout mechanisms for specificity. Base readout in the major groove distinguishes between protein families, while shape readout provides higher resolution specificity within families. DNA shape is influenced by sequence-dependent structural variations, such as DNA bending, A-DNA, Z-DNA, and minor groove narrowing. These structural variations are recognized by proteins, contributing to binding specificity. DNA shape also affects electrostatic potentials, which proteins can read. Proteins use both direct (base-specific hydrogen bonds) and indirect (shape-dependent) readout mechanisms. The review proposes replacing "direct" and "indirect" readout with "base" and "shape" readout, reflecting how proteins recognize DNA sequences. DNA-binding proteins use a range of structural motifs, including helix-turn-helix, winged helix-turn-helix, helix-loop-helix, and beta-sandwich domains. These motifs interact with DNA in the major or minor groove, using hydrogen bonds, hydrophobic contacts, or shape recognition. DNA structure varies sequence-dependent, with B-DNA, A-DNA, Z-DNA, and other conformations. These variations are recognized by proteins, contributing to specificity. DNA bending, kinks, and minor groove narrowing are also recognized by proteins. The review highlights the complexity of protein-DNA recognition, involving multiple readout mechanisms and structural variations in DNA. Understanding these mechanisms is essential for accurately annotating genome sequences and understanding DNA-protein interactions.