Crystal Structure of SRP19 in Complex with the S Domain of SRP RNA and Its Implication for the Assembly of the Signal Recognition Particle  Chris Oubridge, Andreas Kuglstatter, Luca Jovine, Kiyoshi Nagai  Molecular Cell  Volume 9, Issue 6, Pages 1251-1261 (June 2002) DOI: 10.1016/S1097-2765(02)00530-0

Figure 1 The Protein and RNA Components of the Signal Recognition Particle (A) Schematic representation of signal recognition particles from eubacteria (E. coli, left), archaebacteria (M. jannaschii, middle), and mammals (human, right). (B) Amino acid sequence alignment of M. jannaschii (Mj19) and human (Hs19) SRP19 with the secondary structure elements shown below. Green represents positions highly conserved in multiple sequence alignment, and blue represents positions where conservative changes are permitted (Zwieb and Samuelsson, 2000). Closed circles, direct contacts between SRP19 and helix 6; open circles, solvent mediated interaction between SRP19 and helix 6; red circles, contacts conserved between the Hs19-helix 6 complex (Wild et al., 2001) and the Mj19-S domain complex (present work); blue squares, direct contacts between helix 8 and Mj19. Molecular Cell 2002 9, 1251-1261DOI: (10.1016/S1097-2765(02)00530-0)

Figure 2 Experimental Electron Density Map and the Main Chain Trace of M. jannaschii and Human SRP19 (A) Experimental electron density map contoured at 1.5 σ with the refined model in the region of the SRP19-helix 6 interface. The main chain amide group of Ile2 is hydrogen bonded to the phosphate oxygen of A149. The indole nitrogen of Trp4 and the phenolate oxygen of Tyr7 are hydrogen bonded to the 2′OH group of A149 and the phosphate oxygen of G150, respectively. (B) Overlay of the M. jannaschii SRP19 (blue) and the human SRP19 (red) in stereo. The main chain atoms of residues 1–55, 62–65, and 72–82 of Mj19 were superimposed on the corresponding residues of the human SRP19 with an rmsd of 0.98 Å using LSQMAN within O (Jones and Kjeldgaard, 1997). Molecular Cell 2002 9, 1251-1261DOI: (10.1016/S1097-2765(02)00530-0)

Figure 3 The Crystal Structure of the Methanococcus jannaschii SRP19 in Complex with the S Domain of Human 7SL RNA (A) Overview showing coaxially stacked helix 8 and helix 5. Mj19, shown as a blue ribbon, binds to the tetraloops of both helices 6 and 8. Helices 5, 6, and 8 are shown in light blue, light green, and yellow, respectively. (B) Secondary structure of the S domain fragment of human 7SL RNA used for crystallization. RNA is color coded as in (A). The symmetric and asymmetric loops in helix 8 are colored with dark and light orange, respectively. The consecutive AC mismatched base pairs and mismatched AG base pair in helix 6 are highlighted in darker green. The internal loop in helix 5 is highlighted in dark blue. Nucleotides in close helix 6-helix 8 contacts are boxed and joined by broken lines. Two nonnatural Watson-Crick base pairs (outlined character) are added to the ends of the RNA to permit the cleavage by hammerhead ribozyme. Nucleotides protected from hydroxyl radical cleavage in the SRP19-bound form are indicated by red circles (Rose and Weeks, 2001). (C) Surface representation of Mj19 colored according to electrostatic surface potential. Blue, positively charged; red, negatively charged. RNA is shown as a ball-and-stick model. Molecular Cell 2002 9, 1251-1261DOI: (10.1016/S1097-2765(02)00530-0)

Figure 4 The Interaction of Helix 8 with SRP19 and Helix 6 (A) The loop L3 of Mj19 interacting with the minor groove of helix 8. The imidazole ring of His57 is hydrogen bonded to the 2′OH group of U195 and N3 of A205. (B) Interaction between the backbone phosphate groups of the helix 8 tetraloop region and the peptide loop L3 of Mj19. (C) Schematic representation of the tetraloop-tetraloop interaction. (D) Rearrangement of hydrogen bonds in the helix 6 tetraloop upon helix 8 binding. The first and fourth G of helix 6 tetraloop in the Hs19-helix 6 complex (blue) (Wild et al., 2001) and in the Mj19-S domain complex (green) (present work). (E) Symmetric adenine-adenine interaction between the tetraloops of helices 6 and 8. (F) Hydrogen bonding between nucleotides of helices 6 and 8 tetraloops. Protein residues are colored in grey, and helices 6 and 8 are colored in green and yellow, respectively, except in (D). Molecular Cell 2002 9, 1251-1261DOI: (10.1016/S1097-2765(02)00530-0)

Figure 5 Close Interactions between Helices 6 (Green) and 8 (Yellow) (A) Two consecutive AC mismatched base pairs found in helix 6 at the close helix-helix contact. (B) Close helix 6-helix 8 contact near the asymmetric loop of helix 8. Four adenines in helix 8 stack continuously, and A215 is in syn conformation. (C) Close contacts between helices 6 and 8. G188 is in syn conformation and shows unusual base pairing with U211. Molecular Cell 2002 9, 1251-1261DOI: (10.1016/S1097-2765(02)00530-0)

Figure 6 SRP19 Promotes the Binding of SRP54 by Stabilizing the Structure of the Asymmetric Loop in Helix 8 (A) Conformation of the longer 5′ strand of the asymmetric loop in helix 8. (B) A model of the SRP19/SRP54/RNA complex. The E. coli SRP54 M domain (EcFfh-M) was placed into the SRP19-S domain complex structure by overlaying the symmetric loop of the E. coli M domain-RNA complex (Batey et al., 2000) onto the symmetric loop of the Mj19-RNA complex. Red, domain IV of the E. coli 4.5S RNA (Batey et al., 2000); yellow, helix 8 of 7SL RNA in the Mj19-S domain RNA complex; green, helix 6; blue, M. jannaschii SRP19 (Mj19); orange, the M domain of the E. coli Ffh. The structure of the longer 5′ strand of the asymmetric loops is shown as a ball-and-stick model. (C) The asymmetric loop of 4.5S RNA has been shown to undergo a hinge motion by NMR (Schmitz et al., 1999). In the absence of SRP19, helix 6 swings away from helix 8, as indicated by a loss of protection from hydroxyl radical cleavage (Rose and Weeks, 2001). (D) A model of the mammalian SRP. The S domain RNA with SRP19 and the SRP54 M domain are as in (B), and the Alu domain RNA with SRP9/14 heterodimer is based on a model by Weichenrieder et al. (2000). The A form RNA linker between the S and Alu domains (gray) is built as an A form helix with 38 base pairs. Although the structure of the N/G domain of Ffh is known, its position with respect to the M domain is uncertain (Keenan et al., 1998). There is no structural information for the SRP68/72 heterodimer. Approximate length of the model is in good agreement with Andrews et al. (1987). Molecular Cell 2002 9, 1251-1261DOI: (10.1016/S1097-2765(02)00530-0)