Fig. 4: Translocation mechanism for the ϕ29 DNA-packaging motor. | Nature Communications

Fig. 4: Translocation mechanism for the ϕ29 DNA-packaging motor.

From: A DNA packaging motor inchworms along one strand allowing it to adapt to alternative double-helical structures

Fig. 4

The mechanism of the motor packaging (a) dsDNA and (b) dsRNA is shown. For each state, the ring ATPase complex is presented from the side, with each subunit represented as a cylinder with a sphere at its hinge and colored by nucleotide state. The capsid is above in gray and the special subunit is on the left, marked with an S. Tracking strand phosphates are depicted as colored spheres. The states in the dwell are labeled as D1–D6 and the states in the burst are labeled B1–B6. D6 and B1 are the same state, as well as D1 and B6, repeated only for horizontal comparison. Dashed lines with spacing 0.85 nm show the extent of ring opening. One phosphate is colored magenta during the burst to track translocation. During the dwell, ADP exchanges for ATP, which opens the ring. During the burst, ATP hydrolysis drives DNA translocation. It is noteworthy that the first exchange and hydrolysis is in the special subunit, which causes no ring opening or substrate translocation. On dsRNA, the mechanism is identical, except for the final opening and closing steps, which are shorter and are denoted by the red dashed lines. See also Supplementary Movie 1 and 2.

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