Structural studies of an RNA aptamer‐with high affinity for the B. anthracis ribosomal protein S8.

Abstract

The bacterial S8 protein is a ribosomal protein which binds to the 16S rRNA in the central domain and plays a critical role in 30S ribosomal subunit assembly. An RNA aptamer with high affinity for B. anthracis S8 protein was developed using the SELEX methodology and crystals of the complex were obtained. To understand how S8/RNA recognition occurs for this apatamer, we are determining the structure of the complex by X‐ray crystallography. Diffraction data for the S8/RNA crystal were collected to 2.6Å resolution at the Advanced Light Source synchrotron (Berkeley, CA). The crystal belonged to the space group P212121 with unit cell parameters a= 55.41 b=59.27 c=92.25Å, α=90, β= 90, γ=90. The data were processed using the program d*TREK with Rmerge=9.2 % and completeness = 99.9 %. A molecular replacement solution for S8/RNA complex was found with the program Phaser for MR from the CCP4 suite using S8 protein (unpub.data) as a search model. The initial solution suggested one monomer per asymmetric unit consistent with a Matthews coefficient of 3.2 (65% solvent). The molecular replacement solution was further confirmed by the initial (2Fo‐Fc) maps generated using Coot that clearly indicated electron density for the RNA aptamer. A model is being constructed for the protein‐RNA complex. This work was supported by NSF (0641792) to Y.S. and The Robert A. Welch Foundation (C‐1584 to Y.S. and C‐1277 to E.P.N.) and NIH(U54 AI057156).