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![[Figure 7]](yt5100fig7mag.jpg)
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Figure 7
Crystal structure of Aae Hfq with U-rich RNA bound at the lateral rim. The asymmetric unit of the P6 form contains a single Hfq subunit, shown as a tan-colored ribbon diagram (a), in addition to 36 H2O molecules (red spheres), a molecule of PEG (lime-colored C atoms), a molecule of MPD (gray C atoms) and one molecule of U6 RNA (green C atoms). Nonprotein atoms are shown in ball-and-stick representation using CPK colors (except as noted above for C atoms). Expansion of the asymmetric unit to the full P6 cell gives an intact Hfq hexamer, shown on the proximal face in (a). The meshes delimit the 2mFo − DFc electron-density map, contoured at 1.5σ and shown only in the regions of RNA (dark blue) or MPD (light blue). The fragment of U6 that could be unambiguously built into electron density contained two complete uridines and the 5′ phosphate moiety of the next residue; the path of this RNA strand is denoted by a red-circled 1 and 3 for the ribonucleotides, from 5′ to 3′. Unexpectedly, U6 nucleotides were found on the outer rim of Aae Hfq, in a position analogous to the lateral site of other Hfqs (b), while a molecule of MPD occupied the U-rich binding pore as shown in (c). This magnified view (b) of the lateral site [same color scheme as (a)] shows the RNA-contacting residues (labeled) in greater detail; asterisks distinguish residues from the N-termini of a neighboring subunit, as also indicated in (a). Electron-density maps such as this one were readily interpretable as RNA (see also Supplementary Fig. S7). The magenta dashed lines (hydrogen bonds) and semi-transparent green cylinders (π-stacking interactions) indicate enthalpically favorable Hfq⋯RNA contacts. Most such contacts are mediated by both backbone and side-chain atoms of Aae Hfq, as well as the nucleobase and phosphodiester groups of the RNA; the ribose rings project outward from the cleft and interact with Hfq more sparsely. (c) MPD binds at the pore and mimics the Hfq⋯uridine contacts found at the proximal RNA-binding site in some Hfq homologs. Contacts denoted by magenta dashed lines identically match the contacts to a uridine nucleotide in other Hfq structures containing U-rich RNA (see also Supplementary Fig. S8). The green line indicates a van der Waals contact between Leu39 and MPD, and the green cylinder denotes another apolar interaction between Aae Hfq and MPD; this latter contact would presumably be replaced by a π-stacking interaction between Phe40 and a U base, were a U-rich RNA (rather than MPD) bound at the proximal site. |
![[Figure 7]](yt5100fig7.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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