The ribosome at improved resolution: new techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles

The chaperonin ATPase cycle: mechanism of allosteric switching and movements of substrate-binding domains in GroEL

Chaperonin-assisted protein folding proceeds through cycles of ATP binding and hydrolysis by the large chaperonin GroEL, which undergoes major allosteric rearrangements. Interaction between the two back-to-back seven-membered rings of GroEL plays an important role in regulating binding and release of folding substrates and of the small chaperonin GroES. Using cryo-electron microscopy, we have obtained three-dimensional reconstructions to 30 A resolution for GroEL and GroEL-GroES complexes in the presence of ADP, ATP, and the nonhydrolyzable ATP analog, AMP-PNP. Nucleotide binding to the equatorial domains of GroEL causes large rotations of the apical domains, containing the GroES and substrate protein-binding sites. We propose a mechanism for allosteric switching and describe conformational changes that may be involved in critical steps of folding for substrates encapsulated by GroES.

Similar architectures of native and transformed human alpha2-macroglobulin suggest the transformation mechanism

The refined three-dimensional structure of native human alpha2-macroglobulin (alpha2M) has been determined by cryoelectron microscopy and three-dimensional reconstruction. New features corresponding to "sigmoid arches," "basal bodies," and "apical connections" were observed in the molecule. Since similar elements are found in the architecture of transformed alpha2M, the 2 volumes were aligned in three dimensions. In their common orientations, they show many similarities except near the openings of the central chamber. In the native conformation, these apertures are fully opened, allowing the proteases to access the central chamber of the molecule, while in the transformed structure, they are partially closed. These structures suggest that alpha2M conformational change involves a strong lateral compression and a vertical stretching of the native particle seen in its four-petaled flower view to produce the H view of the transformed form. A model of structural transformation, in which all the parts of the alpha2M molecule seem involved in the entrapment of the proteinases is proposed.

A common-lines based method for determining orientations for N > 3 particle projections simultaneously

A method is proposed for determining the directions of projections. An arbitrary number of projections of unknown three-dimensional structure are simultaneously used as input. The method is based on common lines and uses a new discrepancy measure accounting for the uneven distribution of common lines in angular space. An application to the 70S Escherichia coli ribosome data obtained from an energy-filtering electron microscope is described.

Three-dimensional structure of the Z band in a normal mammalian skeletal muscle

The three-dimensional structure of the vertebrate skeletal muscle Z band reflects its function as the muscle component essential for tension transmission between successive sarcomeres. We have investigated this structure as well as that of the nearby I band in a normal, unstimulated mammalian skeletal muscle by tomographic three-dimensional reconstruction from electron micrograph tilt series of sectioned tissue. The three-dimensional Z band structure consists of interdigitating axial filaments from opposite sarcomeres connected every 18 +/- 12 nm (mean +/- SD) to one to four cross-connecting Z-filaments are observed to meet the axial filaments in a fourfold symmetric arrangement. The substantial variation in the spacing between cross-connecting Z-filament to axial filament connection points suggests that the structure of the Z band is not determined solely by the arrangement of alpha-actinin to actin-binding sites along the axial filament. The cross-connecting filaments bind to or form a "relaxed interconnecting body" halfway between the axial filaments. This filamentous body is parallel to the Z band axial filaments and is observed to play an essential role in generating the small square lattice pattern seen in electron micrographs of unstimulated muscle cross sections. This structure is absent in cross section of the Z band from muscles fixed in rigor or in tetanus, suggesting that the Z band lattice must undergo dynamic rearrangement concomitant with crossbridge binding in the A band.

Three-dimensional reconstruction of Macrobdella decora (leech) hemoglobin by cryoelectron microscopy

Macrobdella decora hemoglobin was observed in vitreous ice by cryoelectron microscopy and subjected to three-dimensional reconstruction by the method of random conical tilt series. The refined volume has a resolution of 40 A and a D6 point-group symmetry. Its architecture, with its hexagonal bilayer appearance, resembles those of Lumbricus terrestris (oligochaete) and Eudistylia vancouverii (polychaete). When the reconstruction volume is viewed along its sixfold axis, the vertices of the upper hexagonal layer are rotated 16 degrees clockwise compared to those of the lower layer. In agreement with the "bracelet" model of Vinogradov et al., a central linker complex is decorated by 12 hollow globular substructures. The linker complex is made up of a central hexagonal toroid linked by 12 c5 connections to two bracelets of c3 connections, which are themselves linked via six c4 connections. The portion of the hollow globular substructure corresponding to the dodecamer of globin chains has a local pseudo threefold symmetry and is composed of three elongated structures visible when the volume is displayed at high threshold. The main difference between Macrobdella, Lumbricus, and Eudistylia hemoglobins is the presence in Macrobdella of a central hexagonal toroid instead of a compact flat hexagonal structure.

Direct visualization of A-, P-, and E-site transfer RNAs in the Escherichia coli ribosome

Transfer RNA (tRNA) molecules play a crucial role in protein biosynthesis in all organisms. Their interactions with ribosomes mediate the translation of genetic messages into polypeptides. Three tRNAs bound to the Escherichia coli 70S ribosome were visualized directly with cryoelectron microscopy and three-dimensional reconstruction. The detailed arrangement of A- and P-site tRNAs inferred from this study allows localization of the sites for anticodon interaction and peptide bond formation on the ribosome.

What can electron microscopy tell us about chaperoned protein folding?

Chaperonins form large, cage-like structures that act as protein folding machines. Recent developments in electron cryo-microscopy and image processing are helping to reveal the mechanism of chaperonin-mediated protein folding.

A model of the translational apparatus based on a three-dimensional reconstruction of the Escherichia coli ribosome

The morphology of the Escherichia coli ribosome, i.e., its shape at moderate to low (20-40 A (1 A = 0.1 nm)) resolution, provides important constraints in modeling both the folding of ribosomal RNA and the translational process. A new reconstruction, obtained by low-dose cryoelectron microscopy and image processing of single ribosomes, contains clues to the way in which the ribosome interacts with the key functional ligands: the mRNA and the A- and P-site tRNAs. It also suggests possible pathways of the nascent polypeptide chain. From an interpretation of these clues in the light of existing knowledge, a plausible model for the locations and interactions of key components of protein synthesis is suggested.

Double-tilt electron tomography

Fidelity of tomographic reconstructions is improved and reconstruction artifacts are reduced, without increasing the number of projections, by combining tilt series taken around two orthogonal axes. Test reconstructions were made from high-voltage EM of rat liver mitochondria in a 0.6 micron thick plastic section. A number of schemes for selecting tilt angles for the projections are compared. A new method for aligning fiducial markers is described. It uses an iterative algorithm to determine the shift, scale, in-plane rotation and tilt angle for each tilt image, enforcing agreement of the expected locations of the fiducial markers in 3D space. These 3D locations are used to find the orientation between two tilt series and to merge both sets of projections.

The 70S Escherichia coli ribosome at 23 A 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.

A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome

The ribosome is formed by assembly of proteins and nucleic acids, and synthesizes proteins according to genetic instructions in all organisms. Many of the biochemical steps of this fundamental process are known, but a detailed understanding requires a well-defined structural model of the ribosome. Electron microscopy combined with image reconstruction of two-dimensional crystals or single ribosomes has been the most promising technique, but the resolution of the resulting models has been insufficient. Here we report a 25-A reconstruction of the ribosome from Escherichia coli, obtained by combining 4,300 projections of ice-embedded single particles. Our new reconstruction reveals a channel in the small ribosomal subunit and a bifurcating tunnel in the large subunit which may constitute pathways for the incoming message and the nascent polypeptide chain, respectively. Based on these new findings, a three-dimensional model of the basic framework of protein synthesis is presented.

Structures of small subunit ribosomal RNAs in situ from Escherichia coli and Thermomyces lanuginosus

Small ribosomal subunits from the prokaryote Escherichia coli and the eukaryote Thermomyces lanuginosus were imaged electron spectroscopically, and single particle analysis used to yield three-dimensional reconstructions of the net phosphorus distribution representing the nucleic acid (RNA) backbone. This direct approach showed both ribosomal RNAs to have a three domain structure and other characteristic morphological features. The eukaryotic small ribosomal subunit had a prominent bill present in the head domain, while the prokaryotic subunit had a small vestigial bill. Both ribosomal subunits contained a thick 'collar' central domain which correlates to the site of the evolutionarily conserved ribosomal RNA core, and the location of the majority of ribosomal RNA bases that have been implicated in translation. The reconstruction of the prokaryotic subunit had a prominent protrusion extending from the collar, forming a channel approximately 1.5 nm wide and potentially representing a 'bridge' to the large subunit in the intact monosome. The basal domain of the prokaryotic ribosomal subunit was protein free. In this region of the eukaryotic subunit, there were two basal lobes composed of ribosomal RNA, consistent with previous hypotheses that this is a site for the 'non-conserved core' ribosomal RNA.

A marker-free alignment method for electron tomography

In electron tomography of biological specimens, fiducial markers are normally used to achieve accurate alignment of the input projections. We address the problem of alignment of projections from objects that are freely supported and do not permit the use of markers. To this end we present a new alignment algorithm for single-axis tilt geometry based on the principle of Fourier-space common lines. An iterative scheme has been developed to overcome the noise-sensitivity of the common-line method. This algorithm was used to align a data set that was not amenable to alignment with fiducial markers.

Automatic particle picking from electron micrographs

A computer program for automatic particle picking based on textural methods is proposed. The technique relies on the evaluation of certain textural parameters for data windows containing single particles, and those containing undesirable material. These parameters are manipulated by a discriminant analysis routine for determining the rules of classification between the different categories. The effectiveness of the method was demonstrated by application to electron micrographs of 70S Escherichia coli ribosomes.

Three-dimensional reconstruction of the alpha D and beta C-hemocyanins of Helix pomatia from frozen-hydrated specimens

The three-dimensional (3D) reconstructions of the di-decameric forms of alpha D and beta C-hemocyanins of the Roman snail Helix pomatia and of the decameric half molecules of alpha D-hemocyanin were carried out on frozen-hydrated specimens observed in the electron microscope by using the random conical tilt series method. The three 3D volumes were examined by computing solid-body surface representations and slices through the volume and by eroding the structure progressively through raising of the threshold. The di-decameric molecule of alpha D and beta C-hemocyanins, reconstructed from side views, are very similar and are composed of a cylindrical wall, comprising ten oblique wall units, and of two collar complexes located at both ends of the cylinder, comprising each five arches and an annular collar made up of five collar units. Erosion of the structure reveals that the wall looks like a segment of a five-stranded right-handed helix and that each oblique wall unit resembles a figure 8 inclined to the right. The decameric half molecule of alpha D-hemocyanin, reconstructed from end-on views, resembles the whole molecule, except that the collar is thinner and appears composed of five independent collar complex units. It is suggested that the difference in structural appearance of the collar complex between the whole and the half alpha D-hemocyanin may be due to the missing cone artifact, induced by the angular limitations imposed by the goniometer of the electron microscope. The comparison between the alpha D-hemocyanin and the beta C-di-decameric hemocyanin at high thresholds suggests that in the beta C-hemocyanin the oblique wall units of each half molecule may be linked by two connections, whereas in alpha D-hemocyanin there may be only one. This difference in the number of connections may be responsible for the lower stability of the alpha D molecule at high salt concentration.

Electron cryomicroscopy and angular reconstitution used to visualize the skeletal muscle calcium release channel

We exploit the random orientations of ice-embedded molecules imaged in an electron cryomicroscope to determine the three-dimensional structure of the Ca(2+)-release channel from the sarcoplasmic reticulum (SR) in its closed state, without tilting the specimen holder. Our new reconstruction approach includes an exhaustive search of all different characteristic projection images in the micrographs and the assignment of Euler angle orientations to these views. The 30 A map implied reveals a structure in which the transmembrane region exhibits no apparent opening on the SR lumen side. The extended cytoplasmic region has a hollow appearance and consists, in each monomer, of a clamp-shaped and a handle-shaped domain.