Recognition of Polyadenylate RNA by the Poly(A)-Binding Protein Rahul C Deo, Jeffrey B Bonanno, Nahum Sonenberg, Stephen K Burley  Cell  Volume 98, Issue 6, Pages 835-845 (September 1999) DOI: 10.1016/S0092-8674(00)81517-2

Figure 1 PABP Domain Organization Secondary structural elements were assigned on the basis of the X-ray structure. The RNP motifs are enclosed in boxes. Color coding scheme: lavender, homologous residues; red, side chain–RNA contacts; orange, main chain–RNA contacts. Underlined residues make main chain and/or side chain contacts with the RNA backbone. Functional classifications: π, stacking interaction; 1, N1 hydrogen bond; 2, C2 van der Waals contact; 6, N6 hydrogen bond; 7, N7 hydrogen bond. (A) Sequence alignment of human (h), murine (m), Xenopus (x), Drosophila (d), and yeast (y) PABP RRM1s plus human PABP RRM3 and murine PABII, with their respective sequence numbers. (B) Sequence alignment of PABP RRM2s from the same organisms and human PABP RRM4. (C) Structure-based sequence alignment of U1A, U2B′′, RRM1 and RRM2 of Sex-lethal, and RRM1 and RRM2 of human PABP. (D) Sequence alignment of PABP domain linkers from human, Xenopus, and yeast. (E) Electrophoretic mobility shift assay showing retardation of radiolabeled A25 by human PABP RRM1/2. The last two lanes show the effects of adding a 100-fold excess of unlabeled specific [poly(A)] and nonspecific [poly(C)] RNA competitors. Cell 1999 98, 835-845DOI: (10.1016/S0092-8674(00)81517-2)

Figure 1 PABP Domain Organization Secondary structural elements were assigned on the basis of the X-ray structure. The RNP motifs are enclosed in boxes. Color coding scheme: lavender, homologous residues; red, side chain–RNA contacts; orange, main chain–RNA contacts. Underlined residues make main chain and/or side chain contacts with the RNA backbone. Functional classifications: π, stacking interaction; 1, N1 hydrogen bond; 2, C2 van der Waals contact; 6, N6 hydrogen bond; 7, N7 hydrogen bond. (A) Sequence alignment of human (h), murine (m), Xenopus (x), Drosophila (d), and yeast (y) PABP RRM1s plus human PABP RRM3 and murine PABII, with their respective sequence numbers. (B) Sequence alignment of PABP RRM2s from the same organisms and human PABP RRM4. (C) Structure-based sequence alignment of U1A, U2B′′, RRM1 and RRM2 of Sex-lethal, and RRM1 and RRM2 of human PABP. (D) Sequence alignment of PABP domain linkers from human, Xenopus, and yeast. (E) Electrophoretic mobility shift assay showing retardation of radiolabeled A25 by human PABP RRM1/2. The last two lanes show the effects of adding a 100-fold excess of unlabeled specific [poly(A)] and nonspecific [poly(C)] RNA competitors. Cell 1999 98, 835-845DOI: (10.1016/S0092-8674(00)81517-2)

Figure 1 PABP Domain Organization Secondary structural elements were assigned on the basis of the X-ray structure. The RNP motifs are enclosed in boxes. Color coding scheme: lavender, homologous residues; red, side chain–RNA contacts; orange, main chain–RNA contacts. Underlined residues make main chain and/or side chain contacts with the RNA backbone. Functional classifications: π, stacking interaction; 1, N1 hydrogen bond; 2, C2 van der Waals contact; 6, N6 hydrogen bond; 7, N7 hydrogen bond. (A) Sequence alignment of human (h), murine (m), Xenopus (x), Drosophila (d), and yeast (y) PABP RRM1s plus human PABP RRM3 and murine PABII, with their respective sequence numbers. (B) Sequence alignment of PABP RRM2s from the same organisms and human PABP RRM4. (C) Structure-based sequence alignment of U1A, U2B′′, RRM1 and RRM2 of Sex-lethal, and RRM1 and RRM2 of human PABP. (D) Sequence alignment of PABP domain linkers from human, Xenopus, and yeast. (E) Electrophoretic mobility shift assay showing retardation of radiolabeled A25 by human PABP RRM1/2. The last two lanes show the effects of adding a 100-fold excess of unlabeled specific [poly(A)] and nonspecific [poly(C)] RNA competitors. Cell 1999 98, 835-845DOI: (10.1016/S0092-8674(00)81517-2)

Figure 2 Structure of the Human PABP RRM1/2–RNA Complex (A) RIBBONS (Carson 1991) stereo drawing showing the extended RNA-binding surface created by approximation of RRM1 (red) and RRM2 (blue). Ade-1 to Ade-8, included as an atomic stick figure, is located in the RNA-binding trough. α helices are labeled H1 and H2, and β strands are labeled S1–S4 (′ denotes RRM2). The N and C termini of the protein and the 5′ and 3′ ends of the RNA are labeled. (B) Stereo drawing viewed parallel to the β sheets, showing the extended conformation of the RNA and its interactions with the domain linker (green) and the S2(2′)-S3(3′) loops. (C) Stereo drawing showing the RNA-binding trough. (D) Stereo drawing showing the dorsal surface of the protein, comprised of H1, H2, H1′, and H2′. Cell 1999 98, 835-845DOI: (10.1016/S0092-8674(00)81517-2)

Figure 3 Noncrystallographic Symmetry (A) Protein RIBBONS/RNA stick figure representation of the octameric assembly comprising the asymmetric unit, viewed along the noncrystallographic four-fold axis. Each tandem RRM1/2 is uniquely colored and labeled A–H. (B) View as in Figure 3A with the protein colored according to Figure 2. Cell 1999 98, 835-845DOI: (10.1016/S0092-8674(00)81517-2)

Figure 4 Schematic Representation of RNA–Protein Interactions The β sheets of RRM1 and RRM2 and the domain linker are colored as in Figure 2. Functional classifications: narrow solid lines, van der Waals contacts; narrow broken lines, hydrogen bonds; thick solid lines, protein–base stacking interactions; thick broken lines, base–base stacking interactions. For clarity, close contacts with ribose groups have been omitted. Cell 1999 98, 835-845DOI: (10.1016/S0092-8674(00)81517-2)

Figure 5 Adenine Recognition by PABP RIBBONS/stick figure representation of the interactions between PABP RRM1/2 and polyadenylate RNA. Green dashed lines indicate hydrogen bonds between RNA and protein. (A) Recognition of Ade-1 and Ade-2 by RRM2. (B) Recognition of Ade-3 by RRM2 and part of the RRM2/3 linker. (C) Recognition of Ade-4 and Ade-5 by RRM1, RRM2, and the RRM1/2 linker. (D) Recognition of Ade-6 by RRM1 and the RRM1/2 linker. (E) Recognition of Ade-7 by RRM1, and base stacking with the same base of a protein–RNA complex related by noncrystallographic symmetry (Ade-7′). (F) Recognition of Ade-8 by RRM1. The adenine is sandwiched between the side chain of Tyr-56 and the adenine of a free RNA strand (AdeX). Cell 1999 98, 835-845DOI: (10.1016/S0092-8674(00)81517-2)

Figure 6 Surface Properties of PABP RRM1/2 GRASP (Nicholls et al. 1991) representations of the chemical properties of the solvent-accessible surface of PABP calculated using a water probe radius of 1.4 Å. The surface electrostatic potential is color coded red and blue, representing electrostatic potentials < −20 to >+20 kBT, where kB is the Boltzmann constant and T is the temperature. The calculations were performed with an ionic strength of 0 and dielectric constants of 80 and 2 for solvent and protein, respectively (Gilson et al. 1988). (A) RNA-binding surface of PABP RRM1/2 with poly(A) in the RNA-binding trough. The surface is color coded for electrostatic potential. This view is identical to that shown in Figure 2A. (B) Dorsal surface of PABP RRM1/2, color coded for electrostatic potential. This view is identical to those shown in Figure 2D and Figure 6C. (C) Dorsal surface of PABP RRM1/2, color coded for conservation. Green denotes the surface overlying phylogenetically conserved residues, encompassing a hydrophobic/acidic portion that may be responsible for interactions with eIF4G and PAIP-1. Cell 1999 98, 835-845DOI: (10.1016/S0092-8674(00)81517-2)