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![[Figure 6]](yt5100fig6mag.jpg)
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Figure 6
Structural variation across the Aae Hfq monomer (P6) and dodecamer (P1) crystal forms. At a gross structural level, the two Hfq rings in the head-to-tail dodecamer of the P1 crystal form (Fig. 5 ![[link]](../../../../../../logos/arrows/d_arr.gif) , axial view) appear to be related by a rigid-body rotation. The two rings, the proximal-exposed (PE) and distal-exposed (DE) hexamers, were brought, via pure rigid-body translation, to a common origin, indicated by the blue sphere in (a). Best-fit planes to each ring were then computed as described in §2.6 and shown here as semi-transparent hexagonal plates of either orange (DE ring) or cyan (PE ring) color. For clarity, the DE ring (orange/yellow in Fig. 5) is omitted in (a), and a couple of the L2 loops are labeled (in the PE ring) simply as a structural landmark. The three principal axes of the moment of inertia tensor are shown in either orange (DE ring) or blue (PE ring); large differences in the orientation of these principal axes are marked by green and red `Δ' symbols, while a `δ' symbol (blue) denotes smaller-scale differences. The rotation between the rings is clear from the relative disposition (Δ) of two of the principal axes. Furthermore, a small, but discernable, difference (δ) in the directions of the normal axes indicates a slight tilt between the rings; this direction would correspond to the sixfold axis in a perfectly symmetric double hexamer. A multiple structural alignment of the 12 subunits in the P1 cell (b) reveals little structural variation of the Sm core (shown as Cα backbone traces), while there are many examples of side-chain variability (as noted in the panel). The defining secondary-structural elements of the Sm fold (L1 loop, β1 strand etc.), as well as the termini, are labeled. The two regions of Aae Hfq that most extensively engage in interactions between rings (hexamer–hexamer contacts in Fig. 5), and in forming crystal contacts, are the L4 loops and the irregularly structured ∼5 residues at the N-terminus (preceding α1). These also are the two most variable regions in Hfq, both in terms of sequence length (and composition) as well as three-dimensional structure, as seen in (b). The side-chain variability shown in (b) takes two forms: (i) alternate conformers that could be built for a single residue, such as the Gln52 example highlighted to the left, and (ii) rotameric variation for a single residue across the 12 subunits, such as the groups of three residues shown as sticks near the top of (b). In many instances of the latter case, the 12 residue states clustered into two groups, corresponding to the DE or PE hexamer. In the diagram in (c), the Hfq subunits in P1, labeled by chain ID, are evenly spaced about a circle; arcs are drawn between the most structurally similar pairs of subunits, with the line thickness inversely scaled by the r.m.s.d. for the given pair. For clarity, not all ∼n2 edges are shown here, but rather only at the levels of subunit pairs and triples (i.e. the deepest and second-deepest levels of leaf-nodes in the full dendrogram of Supplementary Fig. S5c). This result, from hierarchical clustering on backbone r.m.s.d.s, shows that pairs of monomers within a given hexamer are structurally more similar to each other than are pairs between hexamers (chains A→F comprise the PE ring and chains G→L comprise the DE ring). |
![[Figure 6]](yt5100fig6.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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