Interaction of signal-recognition particle 54 GTPase domain and signal-recognition particle RNA in the free signal-recognition particle -- Hainzl et al. 104 (38): 14911 Data Supplement - HTML Page - index.htslp -- Proceedings of the National Academy of Sciences

Hainzl et al. 10.1073/pnas.0702467104.

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SI Figure 6
SI Figure 7
SI Figure 8
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SI Figure 6

Fig. 6. Space-filling representation of 7S.S RNA in the free form (Left) (1), the SRP19-bound form (Center) (2), and the SRP54-SRP19-bound form (Right). Shown is how flexibility in the 7S.S RNA precedes protein binding during M. jannaschii SRP assembly. The atoms are colored in a continuum according to their individual temperature factors (B-factors): the smallest values are blue and the highest values are red. The minimum, maximum, and mean B-factor values are ≈10, ≈100, and 38 Å² in the free RNA; ≈5, ≈100, and 44 Å² in the SRP19-RNA complex; and ≈5, ≈65, and 35 Å² in the SRP54-SRP19-RNA complex. The binding sites of the individual SRP proteins are indicated with circles.

1. Hainzl T, Huang S, Sauer-Eriksson AE (2005) RNA 11:1043-1050.

2. Hainzl T, Huang S, Sauer-Eriksson AE (2002) Nature 417:767-771.

SI Figure 7

Fig. 7. NG domain-RNA contacts. (A) Topological diagram of the SRP54 NG domain. The arrows and rectangles represent b-strands and a-helices, respectively. Secondary structural elements belonging to the N, G, and IBD domains are colored in green, blue, and yellow, respectively. Contact regions with the 7S.S RNA are indicated in red. (B) Structure-based sequence alignment of the SRP54 NG domains from different organisms (M. jan, M. jannaschii; A. amb, A. ambivalens; S. solf, S. solfataricus; T. aq, T. aquaticus). Invariant residues are boxed in red. Residue numbering corresponds to M. jannaschii SRP54. The secondary structure elements are indicated. Above the alignment, residues in M. jannaschii S domain A, which are within 3.5 Å (*) and 5 Å (#) of the RNA are marked. Below the alignment, basic residues that are conserved in SRP54 sequences, but not in SR sequences are marked (•). In site-directed hydroxyl radical probing experiments (1), the corresponding residues in E. coli Ffh to those marked (x) did not cleave the 4.5S RNA in the Ffh-4.5S RNA complex. In M. jannaschii S domain A, the distances between these residues and the 7S RNA are 7.1 Å to residue K17 (b-carbon to the nearest RNA backbone atom), 13.5 Å to residue E152, and 10.1 Å to residue K288. Residues K53 and K232 lie on the opposite side of the NG-RNA interface.

1. Spanggord RJ, Siu F, Ke A, Doudna JA (2005) Nat Struct Mol Biol 12:1116-1122.

SI Figure 8

Fig. 8. The C-terminal helix of the NG domain is located in the NG-RNA interface. Two basic residues, Lys-288 and Arg-292, situated on the surface of this helix are conserved in SRP54 but not in SR. In S domain A, these two residues are directed toward the RNA helices 8 and 6. On association with SR, the C-terminal helix shifts independently of the N and G domains (1, 2). In the SRP-SR complex, the conserved basic residues in the C-terminal helix, together with the conserved arginine of the DARGG motif, form a "ladder" of basic residues, which is directed toward the 4.5S RNA/M domain complex (3, 4). The ribbon of the NG domain is shown in blue, and the RNA is shown in red. The protein side chains are shown for the residues in the C-terminal helix only.

1. Egea PF, Shan SO, Napetschnig J, Savage DF, Walter P, Stroud RM (2004) Nature 427:215-221.

2. Focia PJ, Shepotinovskaya IV, Seidler JA, Freymann DM (2004) Science 303:373-377.

3. Spanggord RJ, Siu F, Ke A, Doudna JA (2005) Nat Struct Mol Biol 12:1116-1122.

4. Gawronski-Salerno J, Coon JS, V, Focia PJ, Freymann DM (2007) Proteins 66:984-995.

SI Figure 9

Fig. 9. Conformation of the conserved 292-RLLGMGD motif in S domain A. The motif folds into a sharp ab turn mediated by unfavorable main-chain torsion angles for Gly-295 and Met-296 and stabilized by interactions with the N domain core and RNA. The surface-exposed side chain of Arg-292 is in close contact to the phosphate oxygens of C179 and C180 in helix 6, whereas residues Leu-293 and Leu-294 are packed between aN1 and aN4 of the N domain forming conserved hydrophobic contacts. The linker residue Leu-299 stabilizes the sharp turn by hydrophobic interactions with the side chains of Lys-287 and Tyr-79 in aN4. The quality of the difference electron density map (2|F_o| - |F_c|) in this area is shown and contoured at 1s. The figure was prepared with O (1) and MOLRAY (2).

1. Jones TA, Zou JY, Cowan SW, Kjeldgaard M (1991) Acta Crystallogr A 47:110-119.

2. Harris M, Jones TA (2001) Acta Crystallogr D 57:1201-1203.

SI Figure 10

Fig. 10. Superposition of the SRP54 M domains of M. jannaschii S domain A (blue), B (green), and of the S. solfataricus SRP54-helix 8 complex (red) (1). The figure (top view) shows the different relative orientations of their respective NG domains. The RNA of the M. jannaschii complex is shown as a gray ribbon. SRP19 is omitted for clarity.

1. Rosendal KR, Wild K, Montoya G, Sinning I (2003) Proc Natl Acad Sci USA 100:14701-14706.