RESULTS AND DISCUSSION Structure of L1–mRNA complex Here, we report the crystal structure of ribosomal protein L1 from M.jannaschii in complex with the 49 nt fragment of the M.jannaschii L1 binding site on its mRNA. A stereo view of the complex is shown in Figure 2A. L1 is an elongated molecule with two domains connected by a hinge region. The overall three-dimensional structure of MjaL1 bound with mRNA is close to that of MjaL1 in the isolated state described earlier (2). In both cases, the protein is in the ‘open’ confor- mation and the structure of each domain does not undergo essential conformational change upon complex formation. However, MjaL1 in the mRNA-bound form displays a small (about 2 s) closing of the cavity between the two domains (Figure 2B), which might be dependent on the crystal packing. The protein interacts with RNA mostly through domain I, a ribbon representation of which is given in Figure 2C. The fragment of mRNA is made of two regular double helices separated by a sharp turn (Figures 2 and 3). The ﬁrst of these helices is terminated by the non-canonical A62–G34 base pair, the second one contains a bulged nucleotide A52 and terminates with a tetraloop (the RNA is numbered from the A of the AUG codon, Figure 1). Chain A27–G43 is bent through 90 at position G36 whereas chain C48–C68 forms a loop A58–A61 in the middle part of the fragment. As a result, ribose-phosphate groups of G37 and C63 are brought into proximity. Phosphate groups of nucleotides G34–C38 and U65–C66 are approximately in the same plane and surround a slightly concave region of about 14 · 16 s2 through which mRNA mainly interacts with L1. The surface of the ﬁrst helix of the mRNA fragment is complementary to the surface of the b-sheet of domain I. Two monomers in the asymmetric unit are connected by a non-crystallographic 2-fold axis and have slightly different conformations at the regions of two ﬂexible loops b1–b2 and a8–b9 (Figure 2C), not involved in interactions with mRNA and located in domain I. Superposition of domains I yields an r.m.s. deviation of 0.89 s for all Ca atoms; that of domain II is 0.56 s. The two mRNA molecules have similar conformations with r.m.s. deviation between P atoms of about 0.57 s, whereas those nucleotides that interact with the protein coincide much better (r.m.s. deviation of 0.27 s). Two com- plexes in the asymmetric unit form a tightly associated dimer, where RNA molecules contact each other through the inter- connecting loop and the bulged nucleotide A52. In the crystal, symmetry-related dimers interact through the residues of domain II or making a head-to-tail RNA arrangement. Comparison of the structures of the L1–mRNA and L1–rRNA complexes Earlier, we have published the crystal structure of ribosomal protein L1 from Sulfolobus acidocaldarius in complex with a speciﬁc 55 nt fragment of 23S rRNA from T.thermophilus (5). Now it is possible to compare the structure of the riboso- mal complex L1–rRNA and the structure of the present regu- latory complex L1–mRNA (Figures 3 and 4). The L1 proteins in both complexes have similar overall three-dimensional structures and demonstrate an ‘open’ conformation. Schemes of the secondary and spatial structures of the mRNA and rRNA fragments as well as their ribbon models Nucleic Acids Research, 2005, Vol. 33, No. 2 481 Figure 2. (A) Stereo view of the L1–mRNA complex. The ribose-phosphate backbone is in gold, bases are in green, b-strands in blue and a-helices in red. Conserved nucleotides are shown in magenta and yellow. (B) Superposition of the structures of the isolated MjaL1 protein (gray) and MjaL1 from the present complex (black) with least squares minimization of differences in Ca atom coordinates of domain I. (C) Stereo view of the MjaL1 domain I. are presented in Figure 3. It is seen that the rRNA molecule has a more complicated three-dimensional structure, because of two loops interacting with each other. In mRNA, one of these loops (A), is absent, the other (B) is six residues shorter. In spite of this difference, both RNAs have the same unique region in the junction of two helices. In the rRNA fragment, helices 76 and 77 form a co-axial helix that is perpendicular to