Fig. 3: Comparison between the closed and open SLII conformers. | Nature Communications

Fig. 3: Comparison between the closed and open SLII conformers.

From: Structure of HIV-1 RRE stem-loop II identifies two conformational states of the high-affinity Rev binding site

Fig. 3

A Comparison of the RNA major grooves in the closed and open SLII conformers. In the closed conformer (left), the width of the major groove formed between stems IIA and IIB at the GGG motif is ~12 Å, and the distance between the C1′ atoms of G8 and U35 is ~12 Å. In the open SLII conformer (right), the same major groove is widened to ~17 Å, and the distance between the C1′ atoms of G8 and U35 is widened to ~28 Å. B Alignment of the two conformations at stem IIA. The closed conformer is colored in gray, and the open conformer is colored as in (A). The superposition of closed and open conformers with IIA indicates that opening of the high-affinity Rev-binding site rotates stems IIB by ~28° and IIC by ~65°.

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