Volume 8, Issue 4, Pages (April 2000)

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Volume 8, Issue 4, Pages 363-371 (April 2000) Archaeal ribosomal protein L1: the structure provides new insights into RNA binding of the L1 protein family Natalia Nevskaya, Svetlana Tishchenko, Roman Fedorov, Salam Al-Karadaghi, Anders Liljas, Alex Kraft, Wolfgang Piendl, Maria Garber, Stanislav Nikonov Structure Volume 8, Issue 4, Pages 363-371 (April 2000) DOI: 10.1016/S0969-2126(00)00116-7

Figure 1 Stereoview of part of the electron-density map calculated from DM phases [25] of the ribosomal protein L1 from M. jannaschii. The map is contoured at the 1.2σ level. Structure 2000 8, 363-371DOI: (10.1016/S0969-2126(00)00116-7)

Figure 2 The overall structure of ribosomal protein MjaL1. (a) Stereoview ribbon representation showing the elements of secondary structure: α helices, red; β strands, blue; and 310 helices, orange. (b) Stereoview Cα trace of the MjaL1 backbone with every tenth atom labelled and marked with a closed circle. (The figure was generated using MOLSCRIPT [28].) Structure 2000 8, 363-371DOI: (10.1016/S0969-2126(00)00116-7)

Figure 3 Representative sequences of L1 proteins from two phylogenetic domains: TthL1 (bacteria) and MjaL1 (archaea). The numbering is for MjaL1. Conserved substitutions (Val/Ile/Leu, Thr/Ser, Asp/Glu, Asn/Gln, Arg/Lys, Tyr/Phe) within each domain are indicated by boxes; the boxes are yellow if corresponding residues are identical in all known sequences of the domain. If conserved substitutions or identical residues occur for bacteria and archaea at the same positions they are boxed together. The positions of α helices, 310 helices and β strands of MjaL1 are shown below the alignment. Structure 2000 8, 363-371DOI: (10.1016/S0969-2126(00)00116-7)

Figure 4 The open conformation of MjaL1 is stabilized by a network of hydrogen bonds and salt bridges. Stereoview of MjaL1 with hydrogen bonds and salt bridges shown as dotted lines; key residues are labelled. (This figure was generated using MOLSCRIPT [28].) Structure 2000 8, 363-371DOI: (10.1016/S0969-2126(00)00116-7)

Figure 5 Stereoview superposition of MjaL1 (red) and TthL1 (green) with least-squares minimization of differences in the Cα atom coordinates of the β sheet of domain I. The structures are strikingly different owing to the different relative positions of domain II. MjaL1 has an open conformation in contrast to the conformation of TthL1. Structure 2000 8, 363-371DOI: (10.1016/S0969-2126(00)00116-7)

Figure 6 Clusters of strictly conserved residues of (a) TthL1 and (b) MjaL1. The clusters are close to each other in TthL1, but in MjaL1 they are separated by approximately 25 Å and are fully exposed to RNA due to the open conformation. Conserved residues are shown in red. (This figure was generated using the program MOLSCRIPT [28].) Structure 2000 8, 363-371DOI: (10.1016/S0969-2126(00)00116-7)

Figure 7 The molecular surfaces of (a) TthL1 and (b) MjaL1 coloured by electrostatic potential (red, negative; blue, positive; white, uncharged). A well-defined region of positive charge is seen clearly in domain II of MjaL1. (This figure was generated using WebLab ViewerPro [29].) Structure 2000 8, 363-371DOI: (10.1016/S0969-2126(00)00116-7)