Fig. 4: Interaction between RNA and Vif. | Nature Communications

Fig. 4: Interaction between RNA and Vif.

From: HIV-1 vif mediates ubiquitination of the proximal protomer in the APOBEC3H dimer to induce degradation

Fig. 4

a Superimposed structures of the cpzA3H-VCBC complex (with cpzA3H in green, RNA in yellow and Vif across protomers in pink) and the Vif (blue) and RNA (brown) molecules from the A3G-VCBC complex (PDB ID: 8H0I)20. The RMSD between the two Vif molecules is 0.62 Å. In the cpzA3H-VCBC structure, nucleotides 16–19 from 8H0I’s RNA strand were connected to chain G of cpzA3H-bound dsRNA (this study). b The panel expands on the Vif 161-PPLPS-165 region, showing an adenine molecule (from A3G-VCBC structure) with hydrogen bonds to P164, S165, and K168 (cyan dotted lines). c Electrostatic potential of cpzA3H, cpzA3H-bound dsRNA and Vif, including extended RNA strand from (PDB ID: 8H0I)20 as shown in panel (a). RNA-interacting residues of cpzA3H and Vif form a continuous positively charged surface accommodating the negatively charged RNA. The surface was colored in ChimeraX63 according to the electrostatic potential, ranging from -10.0 kT/e (red) to +10.0 kT/e (blue).

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