Friedrich Zemlin

The 70S Escherichia coli ribosome at 23 å resolution: fitting the ribosomal RNA

BACKGROUND The ribosome--essential for protein synthesis in all organisms--has been an evasive target for structural studies. The best available structures for the 70S Escherichia coli ribosome or its 30S and 50S subunits are based on electron microscopical tilt experiments and are limited in resolution to 28-55 A. The angular reconstitution approach, which exploits the random orientations of particles within a vitreous ice matrix, can be used in conjunction with cryo-electron microscopy to yield a higher-resolution structure. RESULTS Our 23 A resolution map of the 70S ribosome elucidates many structural details, such as an extensive system of channels within the 50S subunit and an intersubunit gap ideally shaped to accommodate two transfer RNA molecules. The resolution achieved is sufficient to allow the preliminary fitting of double-helical regions of an earlier three-dimensional ribosomal RNA model. CONCLUSIONS Although we are still a long way from attaining an atomic-resolution structure of the ribosome, cryo-electron microscopy, in combination with angular reconstitution, is likely to yield three-dimensional maps with gradually increasing resolution. As exemplified by our current 23 A reconstruction, these maps will lead to progressive refinement of models of the ribosomal RNA.

Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex

The mRNA codon in the ribosomal A-site is recognized by aminoacyl-tRNA (aa-tRNA) in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Here we report the 13 Å resolution three-dimensional reconstruction determined by cryo-electron microscopy of the kirromycin-stalled codon-recognition complex. The structure of the ternary complex is distorted by binding of the tRNA anticodon arm in the decoding center. The aa-tRNA interacts with 16S rRNA, helix 69 of 23S rRNA and proteins S12 and L11, while the sarcin-ricin loop of 23S rRNA contacts domain 1 of EF-Tu near the nucleotide-binding pocket. These results provide a detailed snapshot view of an important functional state of the ribosome and suggest mechanisms of decoding and GTPase activation.

Densely packed β-structure at the protein-lipid interface of porin is revealed by high-resolution cryo-electron microscopy

Abstract Porin is an integral membrane protein that forms channels across the outer membrane of Escherichia coli . Electron microscopic studies of negatively stained two-dimensional porin crystals have shown three stain accumulations per porin trimer, revealing the locations of pores spanning the membrane. In this study, reconstituted porin lattices embedded in glucose were investigated using the low-dose technique on a cryo-electron microscope equipped with a helium-cooled superconducting objective lens. The specimen temperature was maintained at 5 K to yield an improved microscopic and specimen stability. Under these conditions, we obtained for the first time electron diffraction patterns from porin lattices to a resolution of 3.2 A and images showing optical diffraction up to a resolution of 4.9 A. Applying correlation averaging techniques to the digitized micrographs, we were able to reconstruct projected images of the porin trimer to a resolution of up to 3.5 A. In the final projection maps, amplitudes from electron diffraction and phases from these images were combined. The predominant feature is a high-density narrow band (about 6 A in thickness) that delineates the outer perimeter of the trimer. Since the molecule consists of almost exclusively β-sheet structure, as revealed by spectroscopic data, we conclude that this band is a cylindrical β-pleated sheet crossing the membrane nearly perpendicularly to its plane. Another intriguing finding is a low-density area (about 70 A 2 ) situated in the centre of the trimer.

Electron radiation damage to protein crystals of bacteriorhodopsin at different temperatures

Abstract A series of diffraction patterns from two-dimensional protein crystals of bacteriorhodopsin (purple membrane) at different temperatures (294 K, 98 K and 4 K) were recorded as the diffraction spots faded due to radiation damage. The patterns were then computationally evaluated in order to obtain a quantitative measurement of the structural preservation while irradiating the specimen. To provide statistically significant results, diffraction spots corresponding to spacings of 3A(1200 spots) and 7A(600 spots) were measured. A substantial increase of the lifetime of high resolution spots was found using liquid nitrogen as a coolant, whereas further structural preservation at liquid helium temperature was significant but smaller. It appears likely therefore that high resolution images are accessible even at liquid nitrogen temperature. Mechanical stability and the absence of thermal specimen drift are certainly of equivalent importance for successful high resolution imaging.