To the editor:

In the October 2002 issue of Nature Structural Biology, Kuglstatter et al.1 presented a crystal structure of the signal-binding domain (also called 'M-domain') of human signal recognition particle (SRP) 54-kDa subunit (SRP54) in complex with 7SL SRP RNA and SRP19. This structure explains many of the biochemical properties of the signal recognition particle. One of the major conclusions of Kuglstatter et al.1 is that SRP54 induces a conformational change in its binding site on 7SL RNA upon binding to the preformed SRP19–RNA binary complex.

Although this conclusion is supported by comparison with a previous crystal structure of the binary complex between SRP19 and SRP RNA2 (see Fig. 1a,b for a schematic diagram), chemical probing results (Fig. 1) from both archaeal3 and human4 SRP19–RNA binary complexes are more consistent with the RNA conformation observed in the crystal structure of the ternary complex than with the crystal structure of the binary complex. These observations raise questions about the biological relevance of the proposed SRP54-induced conformational change.

Figure 1: Schematic representations of the human RNA structure in (a) the SRP19–RNA binary and (b) the SRP54-M–SRP19–RNA ternary complexes in the region of the SRP54 binding site.
figure 1

SRP19-dependent chemical modifications from both Archaeoglobus fulgidus3 and Homo sapiens4 are indicated on the structures: blue, protection from hydroxyl radicals (probes backbone)3,4; red, exposure to diethylpyrocarbonate (indicates base unstacking)3; green, protection from; and yellow, exposure to dimethylsulfate respectively (probes Watson-Crick hydrogen bonding)4. (c) Crystal packing interactions between two symmetry-related molecules in the SRP19–RNA binary complex2. SRP19 is green and 7S RNA is yellow (PDB entry 1L9A).

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Chemical probing clearly supports the formation of the A-minor interactions5,6 in an SRP19-dependent manner. Simultaneous binding of helix 6 and helix 8 by SRP19 likely stimulates formation of the A-minor motifs, which precipitate reorganization of helix 8 to create the SRP54 binding site. Interestingly, a reversed form of the A-minor interactions, in which adenosines from helix 6 contact pyrimidines on helix 8, was observed in a crystal structure of the binary complex of SRP19 and SRP RNA from Methanococcus jannaschii7.

Why, then, does the crystal structure of the binary SRP19–RNA complex not adopt a conformation more like that illustrated in Figure 1b? The answer may lie in crystal packing interactions. In the crystal of the binary complex, the helix 8 SRP54 binding site is intimately involved in packing with a symmetry-related molecule (Fig. 1c). Specifically, Trp58 from SRP19 of one complex in the crystal lattice makes perfect stacking interactions with A184 from the RNA of another complex related by crystallographic symmetry. Thus the structure of the local region of SRP RNA in Figure 1a,c is very likely a minor conformation stabilized by crystal contacts. Binding of the M-domain of SRP54 to form the ternary complex leads to a change in the crystal packing, and ultimately in the space group, from P21212 to P6522.

This discussion raises two points. First, if crystal packing is in fact stabilizing the observed conformation of the binary SRP19–RNA complex, then it is likely that the conformational change proposed by Kuglstatter et al.1 is biologically irrelevant. The biochemical data suggest that binding of SRP19 to the RNA largely reorganizes the asymmetric loop of helix 8 to create something very much like the RNA structure in Figure 1b, thereby greatly enhancing the affinity of SRP54 for a pre-organized SRP RNA. Second, as a general point, if a significant localized conformational change is proposed based on crystallographic structures, then the adjacent crystal contacts should be shown and discussed.

See Reply to "Complex conformations and crystal contacts" by Oubridge et al.