Comparative analysis of ribosome atomic structures deduced computationally from EM images and X-ray structures

Ishida, Hisashi; Matsumoto, Atsushi; Tsutsumi, Yu*; Yura, Kei

We developed an EM density-fitting refinement method to improve the modeled 3D structure of supra-biomolecules by alleviating the steric stress of atoms while retaining the condition that the constituent molecules fit in the EM density map. Our method first uses rigid body fitting to carry out initial fitting and then uses a molecular dynamics (MD) simulation. It was found that (1) the refinement could fit the atomic structure of ribosome into the EM density maps with scores ranging from 68.5 to 83.1%, (2) the movement of the head of the 30S subunit largely contributed to the structural change of the bridge between 30S and 50S ribosome, (3) the bridges in helix 44 of 16S rRNA were well conserved throughout all the structures, (4) there were, at least, five exit tunnels with a diameter more than six angstroms, and (5) the structure of a tunnel was dynamic and its entrance was closed at the initial stage of protein synthesis.