Sequence-Specific RNA Binding by a Nova KH Domain Hal A Lewis, Kiran Musunuru, Kirk B Jensen, Carme Edo, Hua Chen, Robert B Darnell, Stephen K Burley  Cell  Volume 100, Issue 3, Pages 323-332 (February 2000) DOI: 10.1016/S0092-8674(00)80668-6

Figure 1 KH Domain Sequence Alignments Secondary structural elements were assigned on the basis of the X-ray structure. Color coding scheme: yellow, invariant Gly-X-X-Gly motif; red, variable loop; magenta, aliphatic α/β platform. Functional classifications: A, aliphatic stacking interaction; S, side chain–base hydrogen bond, including water-mediated contacts; M, protein backbone–base hydrogen bond; *, van der Waals contact. Sequence alignments of human Nova-1 and Nova-2 KH3, KH1, and KH2, human FMR1 KH1 and KH2 (excluding exon 11), C. elegans GLD-1 KH domain, Drosophila Bicaudal C KH2, E. coli PNP KH domain, and Methanococcus jannaschii NusA KH domain. KH domain point mutants discussed in the text are shown in reverse, with the mutant amino acids listed below. Numbers within variable loop segments denote length of the loop. Cell 2000 100, 323-332DOI: (10.1016/S0092-8674(00)80668-6)

Figure 2 Stem Loop RNA Structures Schematic drawings of the stem loop crystallization RNAs in complexes 1 and 2. Nucleotides making direct protein contacts are denoted with *. Color coding denotes nucleotides making extensive protein contacts (Ade-11 through Cyt-15; magenta, pink, gold, green, and blue) and the remaining nucleotides (gray). Cell 2000 100, 323-332DOI: (10.1016/S0092-8674(00)80668-6)

Figure 3 Structure of the Nova-2 KH3–RNA Complex RIBBONS (Carson 1991) stereodrawings showing color-coded protein (invariant Gly-X-X-Gly motif, yellow; variable loop, red). Crystallization RNA is included as a color-coded atomic stick figure (Figure 2) with a gray ribbon denoting the phosphoribose backbone. α helices are labeled H1, H2, and H3, and β strands are labeled S1, S2, and S3. The N and C termini of the protein, and the 5′ and 3′ ends of the RNA are labeled. All illustrations and contact distances are derived from complex 2. (A) View toward the β sheet face. (B) View toward the α-helical face. (C) View down the axis of α helix H3, showing the jaws of the molecular vise. (D) View toward the aliphatic α/β RNA-binding platform, showing the tetranucleotide gripped by the molecular vise. Cell 2000 100, 323-332DOI: (10.1016/S0092-8674(00)80668-6)

Figure 4 Noncrystallographic Symmetry (A) Protein/RNA RIBBONS representation of the dimeric assembly comprising the asymmetric unit, viewed perpendicular to the noncrystallographic 2-fold axis. The KH domains have been colored as in Figure 6 of Lewis et al., 1999, and the RNA ribbons are color coded as in Figure 2 and Figure 3. (B) Viewed along the noncrystallographic 2-fold axis. Cell 2000 100, 323-332DOI: (10.1016/S0092-8674(00)80668-6)

Figure 5 5′-Ura-Cyt-Ade-Cyt-3′ Binding by Nova-2 KH3 RIBBONS drawings showing the RNA-binding surface sandwiched between the invariant Gly-X-X-Gly motif (yellow) and the variable loop (red). The portion of the stem loop crystallization RNA making extensive protein contacts has been included as a color-coded stick figure (Figure 2) with the aliphatic residues (gray) comprising the hydrophobic α/β RNA binding platform. (A) shows the entire complex. (B), (C), and (D) show the environments of Ade-11 Ura-12, and Cyt-13, respectively. (E) shows the environments of Ade-14 and Cyt-15. The side chain of Leu-28 is denoted with *. (F) corresponds to the views used in (D) and (E), with the overlying RNA removed, and shows the aliphatic platform with the jaws of the molecular vise. Cell 2000 100, 323-332DOI: (10.1016/S0092-8674(00)80668-6)