A method for differentiating proteins from nucleic acids in intermediate-resolution density maps: cryo-electron microscopy defines the quaternary structure of the Escherichia coli 70S ribosome

Background: This study addresses the general problem of dividing a density map of a nucleic-acid-protein complex obtained by cryo-electron microscopy (cryo-EM) or X-ray crystallography into its two components. When the resolu tion of the density map approaches similar to 3 Angstrom it is generally po ssible to interpret its shape (i.e., the envelope obtained for a standard c hoice of threshold) in terms of molecular structure, and assign protein and nucleic acid elements on the basis of their known sequences. The interpret ation of low-resolution maps in terms of proteins and nucleic acid elements of known structure is of increasing importance in the study of large macro molecular complexes, but such analyses are difficult. Results: Here we show that it is possible to separate proteins from nucleic acids in a cryo-EM density map, even at 11.5 Angstrom resolution. This is achieved by analysing the (continuous-valued) densities using the differenc e in scattering density between protein and nucleic acids, the contiguity c onstraints that the image of any nucleic acid molecule must obey, and the k nowledge of the molecular volumes of all proteins. Conclusions: The new method, when applied to an 11.5 Angstrom cryo-EM map o f the Escherichia coli 70S ribosome, reproduces boundary assignments betwee n rRNA and proteins made from higher-resolution X-ray maps of the ribosomal subunits with a high degree of accuracy. Plausible predictions for the pos itions of as yet unassigned proteins and RNA components are also possible. One of the conclusions derived from this separation is that 23S rRNA is sol ely responsible for the catalysis of peptide bond formation. Application of the separation method to any nucleoprotein complex appears feasible.