Structure and Function of Argonaute Proteins Traci M. Tanaka Hall  Structure  Volume 13, Issue 10, Pages 1403-1408 (October 2005) DOI: 10.1016/j.str.2005.08.005 Copyright © 2005 Terms and Conditions

Figure 1 5′ Phosphate Binding Pocket of AfPiwi A divalent metal ion (M) is coordinated by the 5′ phosphate group (5′ P), Q159, the terminal carboxylate of L427, the third phosphate group of the guide RNA (yellow), and a water molecule (wat). Black dashed lines, metal coordination; red dashed lines, hydrogen bonds. (AfPiwi, PDB code 2BGG.) All figures were prepared with PyMol (http://www.pymol.org). Structure 2005 13, 1403-1408DOI: (10.1016/j.str.2005.08.005) Copyright © 2005 Terms and Conditions

Figure 2 Proposed Exit Path for 3′ End of RNA Targets (A) Surface representation of the AfPiwi crystal structure colored by electrostatic potential. (B) Ribbon diagram of the AfPiwi crystal structure oriented as in (A). (C) Surface representation of the PfAgo crystal structure colored by electrostatic potential. (PfAgo, PDB code 1Z25.) (D) Surface representation of a homology model of Drosophila melanogaster Ago2 based on the structure of PfAgo. This model was generated by threading the sequence of DmAgo2 onto the PfAgo structure using SWISS-MODEL (http://www.expasy.org/spdbv/; Guex and Peitsch, 1997) and superimposing the crystal structure of the PAZ domain of DmAgo2 (Song et al., 2003) on the PAZ domain region. For all panels: yellow, RNA strand representing the guide siRNA; pink, RNA strand representing the target RNA. For (A), (C), (D), and Figure 4B, electrostatic potential was calculated with GRASP (Nicholls et al., 1991) and is shown as blue for +10 kT/e and as red for −10 kT/e. Structure 2005 13, 1403-1408DOI: (10.1016/j.str.2005.08.005) Copyright © 2005 Terms and Conditions

Figure 3 Superposition of the Active Sites of PfAgo (Blue) and Bh-RNase HC (Green) RNA strand from the DNA:RNA hybrid in the Bh-RNase HC structure is shown (pink). Water molecules from PfAgo (red) and Bh-RNase HC (dark pink) are shown as spheres. Gray dashed lines, coordination of metal A in PfAgo; red dashed lines, coordination of metals A and B in Bh-RNase HC. (Bh-RNase HC, PDB code 1ZBI.) Structure 2005 13, 1403-1408DOI: (10.1016/j.str.2005.08.005) Copyright © 2005 Terms and Conditions

Figure 4 Complexes of Ago Proteins and Duplex RNA (A) Ribbon diagram of the PfAgo crystal structure with modeled RNA. This protein:RNA model was created by superimposing PfAgo on the crystal structure of AfPiwi with a mimic of the 5′ end of an siRNA paired to a target RNA. The duplex RNA region was extended to the 3′ end of the siRNA by lengthening the A form RNA (Parker et al., 2005; AfPiwi and model RNA coordinates courtesy of D. Barford). Blue, N-terminal domain; red, PAZ domain; green, middle domain; purple, Piwi domain; yellow, guide RNA; pink, target RNA. The arrow next to the PAZ domain indicates possible movement to accommodate the siRNA:target RNA duplex. (B) Surface representation of the PfAgo crystal structure colored by electrostatic potential. Arrows indicate the locations of two possible binding pockets for the 3′ end of the siRNA fully paired to target RNA. The protein is oriented as in (A). Structure 2005 13, 1403-1408DOI: (10.1016/j.str.2005.08.005) Copyright © 2005 Terms and Conditions