Figure 1. (a) A segment of ssDNA taken from the human RP-A SSB structure with ssDNA. Note how irregular the structure is. The nucleotide bases are in a variety of orientations and are accessible to stacking interactions with other bases or with side-chains from the protein. The phosphodiester backbone is also highly irregular and phosphate–phosphate (pink) distances are quite variable. Carbon (yellow), nitrogen (green) and oxygen (red) atoms are shown as spheres. (b) An electrostatic surface representation of the bacteriophage T4 SSB. The ssDNA-binding cleft of the protein is lined with positively charged amino acids (blue) to make interactions with the negatively charged DNA polymer. Negatively charged regions of the protein surface are shown in red and are well away from the ssDNA-binding cleft at the midsection of the protein.

Figure 2. Ribbon diagram of proteins employing the OB fold (yellow). (a) T4 SSB; (b) RP-A; (c) human mitochondrial SSB; (d) telomere end-binding protein. The OB fold is a conserved ssDNA-binding motif observed in many ssDNA-binding proteins. Several examples of how the OB fold is employed are shown. A ssDNA-binding protein can have one OB fold (T4 SSB) or as many as four in the E. coli SSB tetramer. There are also examples of ssDNA-binding proteins that do not have any OB folds (RecA, Figure 3).

Figure 3. A ribbon view of one turn of the RecA filament as seen along the helical axis in the crystal structure of RecA. The structure shown here corresponds to the ‘collapsed’ or ADP filament and has a helical pitch of 6.4 nm and a rise of 0.21 nm per nucleotide. The extended or ATP filament is extended significantly and has a helical pitch of 9.5 nm (six RecA molecules per turn). The extended filament is responsible for homologous strand exchange.