Figure 1. Parallel coiled-coil structure of GCN4 ZIP homodimer (Protein Data Bank (PDB) accession code 1gd2). The main chains of the two peptide chains are represented as ribbons in gray. The side chains participating in the dimer association are represented as stick models with carbon atoms in brown, nitrogen atoms in blue and oxygen atoms in red. The positions of the heptad repeat are labeled a–g. The d-positioned leucines are boxed and highlighted in green with underline. The a-positioned residues are highlighted in blue. Unusually, this GCN4 ZIP motif has a polar asparagine residue in the a position located at the middle of the ZIP motif.

Figure 2. Pap1 bZIP homodimer bound to DNA (PDB accession code 1gd2). The basic region of the ZIP motif is shown in blue and the ZIP motif in green. The double-stranded DNA fragment is shown as a purple stick model. The basic regions that flank the ZIP coiled coil bind DNA with sequence-specific interactions.

Figure 3. Interchain polar interactions found in the coiled-coil structure of the Fos–Jun ZIP heterodimer (PDB accession code 1fos). Hydrogen bonding interactions are indicated by dotted lines. The dimerization specificity is primary determined by polar interactions involving the side chains of residues at the e and g positions. A few polar residues at the a positions also contribute to the specificity.

Figure 4. Internal interactions of polar residues in a and d positions in the coiled-coil structure of the Pap1 ZIP dimer. Part of the coiled-coil structure is presented to show that His115 in the a position and Thr118 in the d position form water-mediated hydrogen bonds at the coiled-coil interface. Polar residues Asn122 in the a position and Asp123 in the g position also form interchain hydrogen bonds.