Fig. 3: Comparison of ssDNA binding in the inactive open spiral and active closed-ring states of the gp41 helicase.
From: Structural basis of the T4 bacteriophage primosome assembly and primer synthesis
a The ssDNA backbone is sandwiched in the gp41 CTD between the tip of the α-helix following L1 loop (blue) and L2 loop (green). b Superimposition of the ssDNA in the two states demonstrates that the ssDNA end moves by as much as 9 Å to adopt a flatter conformation in the closed-ring state. c Top view of the gp41 helicase showing the coiled ssDNA in the central channel stabilized by the gp41 CTDs. The ssDNA interacts with five gp41 CTDs in the open state (d), and with six gp41 CTDs in the closed state (e). The DNA interacting loops are between the two concentric dotted circles and shown in cartoons. The DNA bases are shown in cartoon and in sticks. f Superimposition of the ssDNA in the T4 helicase with ssDNA inside the T7 gp4 (PDB entry 6N9V), bacterial DnaB (PDB entry 4ESV), and yeast CMG helicase (PDB entry 5U8T). These ssDNA adopt a B-DNA-like configuration with a similar diameter of ~23 Å.
