Structural Basis for Sequence-Nonspecific Recognition of 5′-Capped mRNA by a Cap- Modifying Enzyme  Alec E. Hodel, Paul D. Gershon, Florante A. Quiocho  Molecular Cell  Volume 1, Issue 3, Pages 443-447 (February 1998) DOI: 10.1016/S1097-2765(00)80044-1

Figure 1 Electron Density for the First Trimer of RNA Bound in the Methyltransferase Active Site The 2.7 Å density is calculated as a 2Fo − Fc map using only the protein model to calculate the phases. Contoured at 1σ, only the density near the RNA is displayed for clarity. The surrounding atoms of the protein are shown without density for context. This figure was rendered using RIBBONS (Carson 1991). Molecular Cell 1998 1, 443-447DOI: (10.1016/S1097-2765(00)80044-1)

Figure 2 mRNA–VP39 Complex (A) Stick model showing RNA bound to the active site cleft of VP39. The protein is rendered as a solvent-accessible surface. The sulfur atom of AdoHcy (colored green and labeled with an arrow) defines the methyltransferase active site. (B) The two RNA contacts mapped on a single VP39 molecule resulting from the interaction of the RNA with two symmetry-related protein molecules. The protein is rendered as a transparent solvent-accessible surface. Shown in front of the protein is the second trimer (A4-A5-A6) binding site based on the interactions with a symmetry-related molecule. Behind the protein are the 5′ cap and the first trimer (G1-A2-A3) of the transcript bound in the methyltransferase active site. (C) The proximity of the second RNA contact site to the VP55 dimerization interface. The major red patch denotes surface residues defined in Shi et al. 1997 as the VP55 dimerization 'hot spot.' The smaller red patch (R107 to the right) is another part of the dimerization interface (seeShi et al. 1997). This figure was produced using GRASP (Nicholls et al. 1991). Molecular Cell 1998 1, 443-447DOI: (10.1016/S1097-2765(00)80044-1)

Figure 3 Details of the Interaction between the RNA and the Protein (A)–(D) show stereo stick models of the structure with the following color scheme: carbon is white for the first protein molecule, green for the symmetry mate; oxygen is red; nitrogen is blue; phosphorous is pink; and sulfur is yellow. (A) The 5′ cap triphosphate bridge and the methyltransferase active site. (B) The first trimer of RNA. (C) The second trimer of RNA binding to a symmetrically related protein molecule. (D) The residues at the methyltransferase active site. S-adenosylmethionine (in green) is fit to AdoHcy in the structure. The donor methyl group is connected to the target hydroxyl by a dashed yellow line. The hydrogen bond between K175 and the target hydroxyl is also shown. (E) A schematic representation of the RNA showing hydrogen bonds with the protein as dashed lines. Residues from one protein molecule are shown in black lettering, whereas residues from the symmetry-related protein molecule are shown in outlined lettering. (A)–(D) were rendered using MIDAS (Huang, et al. 1991). Molecular Cell 1998 1, 443-447DOI: (10.1016/S1097-2765(00)80044-1)