Figure 6.

Comparison of the properties of the OB₁ and OB₂ β-barrels. Surface representation of the two N-terminal OB domains of S1 bound to the β-subunit presented in white cartoon. Panels A–C illustrate OB₁, while panels D–F show OB₂. (A and D) Conservation scores of OB₁ and OB₂ generated using the ConSurf server. Dark green: strictly conserved, lighter green: highly conserved and grey: not conserved. (B and E) Electrostatic surface potentials calculated using the APBS Pymol plugin and mapped onto the separate OB domains. These are shown from negative k_bT/e_c = –4 (red) to positive k_bT/e_c = 4 (blue), where k_b, T and e_c are the Boltzmann's constant, absolute temperature and the charge of an electron, respectively. (C and F) A sequence alignment of the six OB domains of ribosomal protein S1 (OB_1–6) was prepared (lower part of the figure) and the residues involved in formation of the β-barrel are highlighted in purple, while the residues with an involvement in general RNA-binding in OB_3–6 are coloured blue. Based on this information, the putative RNA-binding residues in OB₁ and OB₂ are coloured green and mapped onto the OB domains (purple).