Processing images of helical structures: a new twist

High-resolution archaellum structure reveals a conserved metal-binding site

Many archaea swim by means of archaella. While the archaellum is similar in function to its bacterial counterpart, its structure, composition, and evolution are fundamentally different. Archaella are related to archaeal and bacterial type IV pili. Despite recent advances, our understanding of molecular processes governing archaellum assembly and stability is still incomplete. Here, we determine the structures of Methanococcus archaella by X‐ray crystallography and cryo‐EM. The crystal structure of Methanocaldococcus jannaschii FlaB1 is the first and only crystal structure of any archaellin to date at a resolution of 1.5 Å, which is put into biological context by a cryo‐EM reconstruction from Methanococcus maripaludis archaella at 4 Å resolution created with helical single‐particle analysis. Our results indicate that the archaellum is predominantly composed of FlaB1. We identify N‐linked glycosylation by cryo‐EM and mass spectrometry. The crystal structure reveals a highly conserved metal‐binding site, which is validated by mass spectrometry and electron energy‐loss spectroscopy. We show in vitro that the metal‐binding site, which appears to be a widespread property of archaellin, is required for filament integrity.

Visualizing the bacterial cell surface: an overview

The ultrastructure of bacteria is only accessible by electron microscopy. Our insights into the architecture of cells and cellular compartments such as the envelope and appendages is thus dependent on the progress of preparative and imaging techniques in electron microscopy. Here, I give a short overview of the development and characteristics of methods applied for imaging (components of) the bacterial surface and refer to key investigations and exemplary results. In the beginning of electron microscopy, fixation of biological material and staining for contrast enhancement were the standard techniques. The results from freeze-etching, metal shadowing and from ultrathin-sections of plastic-embedded material shaped our view of the cellular organization of bacteria. The introduction of cryo-preparations, keeping samples in their natural environment, and three-dimensional (3D) electron microscopy of isolated protein complexes and intact cells opened the door to a new dimension and has provided insight into the native structure of macromolecules and the in situ organization of cells at molecular resolution. Cryo-electron microscopy of single particles, together with other methods of structure determination, and cellular cryo-electron tomography will provide us with a quasi-atomic model of the bacterial cell surface in the years to come.

Unperturbing a non-helically perturbed bacterial flagellar filament: Salmonella typhimurium SJW23

Salmonella typhimurium SJW23 has a right-handed, non-helically perturbed filament of serotype gt with a unique surface pattern. Non-helical perturbations involve symmetry reduction along the five-start helical lines resulting in layer lines of fractional Bessel orders and a consequent seam. The flagellin gene, fliC(23), which we sequenced, differs from the sequence of the canonic, plain SJW1655 flagellin, fliC(1655). We modified discrete components of fliC(23) in order to localize, in the expressed filament, the submolecular site responsible for the non-helical perturbation. These modifications include (i) deleting the outermost domain D3(23), (ii) replacing D3(23) with D3(1655), (iii) substituting a hydrophilic α-helix at the interface between the neighboring domains D1 and D2 with a hydrophobic one from fliC(1655), and (iv) substituting a serine/glycine pair in the loop connecting the modified α-helix to its neighbor; these modifications were made in the presence and absence of D3(23). We used S. typhimurium SJW1655 both as a reference and as a source for 'spare parts'. The symmetry of the constructs was assessed from the power spectra through changes in the layer lines at a height of 1/105 and 1/35 Å(-1), unique to the non-helical perturbation. Deleting D3(23), either alone or in combination with various substitutions, or replacing it with D3(1655) transforms the non-helically perturbed filament into a plain one as judged by the disappearance of the typical layer lines from the power spectra. We conclude that the non-helical perturbation is a product of unique interactions in the D3(23) density shell. Whereas other minor structural changes may occur at the filaments interior, they are all helically symmetric.

3D electron microscopy of biological nanomachines: principles and applications

Transmission electron microscopy is a powerful technique for studying the three-dimensional (3D) structure of a wide range of biological specimens. Knowledge of this structure is crucial for fully understanding complex relationships among macromolecular complexes and organelles in living cells. In this paper, we present the principles and main application domains of 3D transmission electron microscopy in structural biology. Moreover, we survey current developments needed in this field, and discuss the close relationship of 3D transmission electron microscopy with other experimental techniques aimed at obtaining structural and dynamical information from the scale of whole living cells to atomic structure of macromolecular complexes.

High-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus

The treatment of helical objects as a string of single particles has become an established technique to resolve their three-dimensional (3D) structure using electron cryo-microscopy. It can be applied to a wide range of helical particles such as viruses, microtubules and helical filaments. We have made improvements to this approach using Tobacco Mosaic Virus (TMV) as a test specimen and obtained a map from 210,000 asymmetric units at a resolution better than 5 A. This was made possible by performing a full correction of the contrast transfer function of the microscope. Alignment of helical segments was helped by constraints derived from the helical symmetry of the virus. Furthermore, symmetrization was implemented by multiple inclusions of symmetry-related views in the 3D reconstruction. We used the density map to build an atomic model of TMV. The model was refined using a real-space refinement strategy that accommodates multiple conformers. The atomic model shows significant deviations from the deposited model for the helical form of TMV at the lower-radius region (residues 88 to 109). This region appears more ordered with well-defined secondary structure, compared with the earlier helical structure. The RNA phosphate backbone is sandwiched between two arginine side-chains, stabilizing the interaction between RNA and coat protein. A cluster of two or three carboxylates is buried in a hydrophobic environment isolating it from neighboring subunits. These carboxylates may represent the so-called Caspar carboxylates that form a metastable switch for viral disassembly. Overall, the observed differences suggest that the new model represents a different, more stable state of the virus, compared with the earlier published model.

Application of the iterative helical real-space reconstruction method to large membranous tubular crystals of P-type ATPases

Since the development of three-dimensional helical reconstruction methods in the 1960's, advances in Fourier-Bessel methods have facilitated structure determination to near-atomic resolution. A recently developed iterative helical real-space reconstruction (IHRSR) method provides an alternative that uses single-particle analysis in conjunction with the imposition of helical symmetry. In this work, we have adapted the IHRSR algorithm to work with frozen-hydrated tubular crystals of P-type ATPases. In particular, we have implemented layer-line filtering to improve the signal-to-noise ratio, Wiener-filtering to compensate for the contrast transfer function, solvent flattening to improve reference reconstructions, out-of-plane tilt compensation to deal with flexibility in three dimensions, systematic calculation of Fourier shell correlations to track the progress of the refinement, and tools to control parameters as the refinement progresses. We have tested this procedure on datasets from Na(+)/K(+)-ATPase, rabbit skeletal Ca(2+)-ATPase and scallop Ca(2+)-ATPase in order to evaluate the potential for sub-nanometer resolution as well as the robustness in the presence of disorder. We found that Fourier-Bessel methods perform better for well-ordered samples of skeletal Ca(2+)-ATPase and Na(+)/K(+)-ATPase, although improvements to IHRSR are discussed that should reduce this disparity. On the other hand, IHRSR was very effective for scallop Ca(2+)-ATPase, which was too disordered to analyze by Fourier-Bessel methods.

Refining the structure of the Halobacterium salinarum flagellar filament using the iterative helical real space reconstruction method: insights into polymorphism

The eubacterial flagellar filament is an external, self-assembling, helical polymer approximately 220 A in diameter constructed from a highly conserved monomer, flagellin, which polymerizes externally at the distal end. The archaeal filament is only approximately 100 A in diameter, assembles at the proximal end and is constructed from different, glycosylated flagellins. Although the phenomenology of swimming is similar to that of eubacteria, the symmetry of the archebacterial filament is entirely different. Here, we extend our previous study on the flagellar coiled filament structure of strain R1M1 of Halobacterium salinarum. We use strain M175 of H.salinarum, which forms poly-flagellar bundles at high yield which, under conditions of relatively low ionic-strength (0.8 M versus 5 M) and low pH ( approximately 2.5 versus approximately 6.8), form straight filaments. We demonstrated previously that a single-particle approach to helical reconstruction has many advantages over conventional Fourier-Bessel methods when dealing with variable helical symmetry and heterogeneity. We show here that when this method is applied to the ordered helical structure of the archebacterial uncoiled flagellar filament, significant extensions in resolution can be obtained readily when compared to applying traditional helical techniques. The filament population can be separated into classes of different morphologies, which may represent polymorphic states. Using cryo-negatively stained images, a resolution of approximately 10-15 A has been achieved. Single alpha-helices can be fit into the reconstruction, supporting the proposed similarity of the structure to that of type IV bacterial pili.

An iterative Fourier–Bessel algorithm for reconstruction of helical structures with severe Bessel overlap

Classical Fourier-Bessel methodology fails when used to reconstruct helical structures with severe Bessel overlap on the layer lines. In the reconstruction of a peculiar type of double-layered helical tube of GDP-tubulin, we face the problem of Bessel overlap on all the layer lines due to the superposition of the Fourier components from the inner and outer layers of the tube. In order to decompose the Fourier terms of the inner and outer layers more than one image of the tubes must be combined and the orientations of their inner and outer layer helices must be determined. While there is no direct analytical method to determine these orientational parameters, we have devised an iterative Fourier-Bessel algorithm to calculate the correct orientations and thus allow us to obtain a reconstruction from multiple images of the double-layered tubes. The algorithm successfully works for the reconstruction of computer-modeled double-layered helical tubes as well as with real images obtained by cryo-electron microscopy. The algorithm has also been applied with very satisfactory results to the reconstruction of 13-protofilament microtubules, which is another helical structure that suffer Bessel overlap, suggesting its generality.

Windex: a toolset for indexing helices

We describe here a set of procedures and algorithms that may be used as an aid in determining the indexing rule of a helical specimen. Crystallizing macromolecules into helical arrays has the potential to speed up and simplify the process of three-dimensional reconstruction of the macromolecular structure. The process of helical reconstruction has been largely automated except for the critical first step of indexing the helical diffraction pattern. This is quite often the rate-limiting step in the overall process, particularly in the case of large helical tubes, which have complicated helical diffraction patterns that may vary from tube to tube. We have developed a set of procedures, supported by a graphical user interface, that provide a straightforward and semi-automated approach to indexing a helical structure. The new procedures have been tested using a number of helical specimens, including TMV, acto-myosin, decorated microtubules, and a variety of helical tubes of a bacterial membrane protein.

Myo1c is designed for the adaptation response in the inner ear

The molecular motor, Myo1c, a member of the myosin family, is widely expressed in vertebrate tissues. Its presence at strategic places in the stereocilia of the hair cells in the inner ear and studies using transgenic mice expressing a mutant Myo1c that can be selectively inhibited implicate it as the mediator of slow adaptation of mechanoelectrical transduction, which is required for balance. Here, we have studied the structural, mechanical and biochemical properties of Myo1c to gain an insight into how this molecular motor works. Our results support a model in which Myo1c possesses a strain-sensing ADP-release mechanism, which allows it to adapt to mechanical load.

Regulation of KinI kinesin ATPase activity by binding to the microtubule lattice

KinI kinesins are important in regulating the complex dynamics of the microtubule cytoskeleton. They are unusual in that they depolymerize, rather than move along microtubules. To determine the attributes of KinIs that distinguish them from translocating kinesins, we examined the ATPase activity, microtubule affinity, and three-dimensional microtubule-bound structure of a minimal KinI motor domain. Together, the kinetic, affinity, and structural data lead to the conclusion that on binding to the microtubule lattice, KinIs release ADP and enter a stable, low-affinity, regulated state, from which they do not readily progress through the ATPase cycle. This state may favor detachment, or diffusion of the KinI to its site of action, the microtubule ends. Unlike conventional translocating kinesins, which are microtubule lattice–stimulated ATPases, it seems that with KinIs, nucleotide-mediated modulation of tubulin affinity is only possible when it is coupled to protofilament deformation. This provides an elegant mechanistic basis for their unique depolymerizing activity.

MAP2 and tau bind longitudinally along the outer ridges of microtubule protofilaments

MAP2 and tau exhibit microtubule-stabilizing activities that are implicated in the development and maintenance of neuronal axons and dendrites. The proteins share a homologous COOH-terminal domain, composed of three or four microtubule binding repeats separated by inter-repeats (IRs). To investigate how MAP2 and tau stabilize microtubules, we calculated 3D maps of microtubules fully decorated with MAP2c or tau using cryo-EM and helical image analysis. Comparing these maps with an undecorated microtubule map revealed additional densities along protofilament ridges on the microtubule exterior, indicating that MAP2c and tau form an ordered structure when they bind microtubules. Localization of undecagold attached to the second IR of MAP2c showed that IRs also lie along the ridges, not between protofilaments. The densities attributable to the microtubule-associated proteins lie in close proximity to helices 11 and 12 and the COOH terminus of tubulin. Our data further suggest that the evolutionarily maintained differences observed in the repeat domain may be important for the specific targeting of different repeats to either alpha or beta tubulin. These results provide strong evidence suggesting that MAP2c and tau stabilize microtubules by binding along individual protofilaments, possibly by bridging the tubulin interfaces.

Structure determination of tubular crystals of membrane proteins. III. Solvent flattening

Solvent flattening is considered to be a principal means for improving the data quality in X-ray crystallography. It could be equally effective for tubular crystals of membrane proteins imaged by electron microscopy because of the large empty space inside the tubes. However, tubular crystals are difficult objects for solvent flattening due to lack of electron diffraction amplitudes. Therefore, solvent flattening was used to align images more accurately and to improve the completeness of the data by reducing contributions of noise in the solvent (+ lipid) region. The methods developed were tested with the tubular crystals of Ca2+-ATPase embedded in amorphous ice. The improvement of the data quality was remarkable when solvent flattening was applied to many individual images before averaging. In this way, noises contaminated in the protein region by contrast transfer function were removed effectively. Solvent flattening was far more powerful than simple averaging described in Part II of this series (K. Yonekura, C. Toyoshima, Ultramicroscopy 84 (2000) 15).

Structure determination of tubular crystals of membrane proteins. II. Averaging of tubular crystals of different helical classes

A set of programs has been developed for averaging the data from tubular crystals belonging to different helical classes. This was done either by (i) cutting out molecules constituting a unit cell from density maps, and aligning and averaging them in real space; (ii) transforming the densities in a unit cell to layer-line data according to a (possibly artificial) helical symmetry, aligning and averaging them in reciprocal space. These methods were applied to tubular crystals of Ca2+-ATPase. Either method worked well and substantially improved the data quality. Transforming the reconstructed images to the layer-line data has many advantages and is essential for fully exploiting the power of averaging.

The bacterial flagella motor

The bacterial flagellum is probably the most complex organelle found in bacteria. Although the ribosome may be made of slightly more subunits, the bacterial flagellum is a more organized and complex structure. The limited number of flagella must be targeted to the correct place on the cell membrane and a structure with cytoplasmic, cytoplasmic membrane, outer membrane and extracellular components must be assembled. The process of controlled transcription and assembly is still not fully understood. Once assembled, the motor complex in the cytoplasmic membrane rotates, driven by the transmembrane ion gradient, at speeds that can reach many 100 Hz, driving the bacterial cell at several body lengths a second. This coupling of an electrochemical gradient to mechanical rotational work is another fascinating feature of the bacterial motor. A significant percentage of a bacterium's energy may be used in synthesizing the complex structure of the flagellum and driving its rotation. Although patterns of swimming may be random in uniform environments, in the natural environment, where cells are confronted with gradients of metabolites and toxins, motility is used to move bacteria towards their optimum environment for growth and survival. A sensory system therefore controls the switching frequency of the rotating flagellum. This review deals primarily with the structure and operation of the bacterial flagellum. There has been a great deal of research in this area over the past 20 years and only some of this has been included. We apologize in advance if certain areas are covered rather thinly, but hope that interested readers will look at the excellent detailed reviews on those areas cited at those points.

Motor protein decoration of microtubules grown in high salt conditions reveals the presence of mixed lattices

We have used back-projection methods to obtain three-dimensional maps of motor-protein decorated nine and ten protofilament microtubules polymerized in the presence of high salt and preserved in vitreous ice. The resulting three-dimensional maps show that the vast majority of these microtubules have multiple seams, rather than being helical as would be expected according to the lattice accommodation model. These results indicate that microtubules should be analyzed by back-projection before using helical reconstruction approaches, and that nine and ten protofilament microtubules polymerized in high salt conditions are not suitable for helical analysis.

Structural invariance of constitutively active and inactive mutants of acanthamoeba myosin IC bound to F-actin in the rigor and ADP-bound states

The three single-headed monomeric myosin I isozymes of Acanthamoeba castellanii (AMIs)-AMIA, AMIB, and AMIC-are among the best-studied of all myosins. We have used AMIC to study structural correlates of myosin's actin-activated ATPase. This activity is normally controlled by phosphorylation of Ser-329, but AMIC may be switched into constitutively active or inactive states by substituting this residue with Glu or Ala, respectively. To determine whether activation status is reflected in structural differences in the mode of attachment of myosin to actin, these mutant myosins were bound to actin filaments in the absence of nucleotide (rigor state) and visualized at 24-A resolution by using cryoelectron microscopy and image reconstruction. No such difference was observed. Consequently, we suggest that regulation may be affected not by altering the static (time-averaged) structure of AMIC but by modulating its dynamic properties, i.e., molecular breathing. The tail domain of vertebrate intestinal brush-border myosin I has been observed to swing through 31 degrees on binding of ADP. However, it was predicted on grounds of differing kinetics that any such effects with AMIC should be small [Jontes, J. D., Ostap, E. M., Pollard, T. D. & Milligan, R. A. (1998) J. Cell Biol. 141, 155-162]. We have confirmed this hypothesis by observing actin-associated AMIC in its ADP-bound state. Finally, we compared AMIC to brush-border myosin I and AMIB, which were previously studied under similar conditions. In each case, the shape and angle of attachment to F-actin of the catalytic domain is largely conserved, but the domain structure and disposition of the tail is distinctively different for each myosin.

Lipid nanotubes as substrates for helical crystallization of macromolecules

A general approach for crystallization of proteins in a fast and simple manner would be of immense interest to biologists studying protein structure-function relationships. Here, we describe a method that we have developed for promoting the formation of helical arrays of proteins and macromolecular assemblies. Electron micrographs of the arrays are suitable for helical image analysis and three-dimensional reconstruction. We show that hydrated mixtures of the glycolipid galactosylceramide (GalCer) and derivatized lipids or charged lipids form unilamellar nanotubules. The tubules bind proteins in a specific manner via high affinity ligands on the polar head groups of the lipid or via electrostatic interactions. By doping the GalCer with a novel nickel-containing lipid, we have been able to form helical arrays of two histidine-tagged proteins. Similarly, doping with a biotinylated lipid allows crystallization of streptavidin. Finally, three proteins with affinity for positively or negatively charged lipid layers formed helical arrays on appropriately charged tubules. The generality of this method may allow a wide variety of proteins to be crystallized on lipid nanotubes under physiological conditions.

Distortion correction of tubular crystals: improvements in the acetylcholine receptor structure

Biological molecules often crystallize either as tubes, having helical symmetry, or as two-dimensional sheets. Both sorts of crystal are potentially suitable for structure determination to atomic resolution by electron crystallography, but their lattice distortions must first be corrected. We have developed a procedure for tubular crystals, based on independent alignment of very short segments against a reference structure, that allows accurate determination and correction of distortions in all three dimensions. Application of this procedure to images used previously to determine the 9 A structure of the acetylcholine receptor showed that about half of the signal loss caused by the distortions arises from effects correctable in the image plane (bending, changes in scale) and half from effects requiring out-of-plane correction (variations in tilt and in twist around the tube axis). By dividing the tubes into short segments (of lengths about equal to their diameter) it became possible to recover almost all of this loss without reducing appreciably the accuracy in the segmental alignments. The signal retention improved by only 10% at low resolution (20 A), but by progressively greater amounts at higher resolutions, up to approximately 40% at 9 A. As a result the finer structural details were more clearly resolved. With images of better electron-optical quality, much greater gains in signal retention should be obtained.

Evidence for a conformational change in actin induced by fimbrin (N375) binding

Fimbrin belongs to a superfamily of actin cross-linking proteins that share a conserved 27-kD actin-binding domain. This domain contains a tandem duplication of a sequence that is homologous to calponin. Calponin homology (CH) domains not only cross-link actin filaments into bundles and networks, but they also bind intermediate filaments and some signal transduction proteins to the actin cytoskeleton. This fundamental role of CH domains as a widely used actin-binding domain underlines the necessity to understand their structural interaction with actin. Using electron cryomicroscopy, we have determined the three-dimensional structure of F-actin and F-actin decorated with the NH2-terminal CH domains of fimbrin (N375). In a difference map between actin filaments and N375-decorated actin, one end of N375 is bound to a concave surface formed between actin subdomains 1 and 2 on two neighboring actin monomers. In addition, a fit of the atomic model for the actin filament to the maps reveals the actin residues that line, the binding surface. The binding of N375 changes actin, which we interpret as a movement of subdomain 1 away from the bound N375. This change in actin structure may affect its affinity for other actin-binding proteins and may be part of the regulation of the cytoskeleton itself. Difference maps between actin and actin decorated with other proteins provides a way to look for novel structural changes in actin.

A minimal motor domain from chicken skeletal muscle myosin

The myosin head (S1) consists of a wide, globular region that contains the actin- and nucleotide-binding sites and an alpha-helical, extended region that is stabilized by the presence of two classes of light chains. The essential light chain abuts the globular domain, whereas the regulatory light chain lies near the head-rod junction of myosin. Removal of the essential light chain by a mild denaturant exposes the underlying heavy chain to proteolysis by chymotrypsin. The cleaved fragment, or "motor domain" (MD), migrates as a single band on SDS-polyacrylamide gel electrophoresis, with a slightly greater mobility than S1 prepared by papain or chymotrypsin. Three-dimensional image analysis of actin filaments decorated with MD reveals a structure similar to S1, but shorter by an amount consistent with the absence of a light chain-binding domain. The actin-activated MgATPase activity of MD is similar to that of S1 in Vmax and Km. But the ability of MD to move actin filaments in a motility assay is considerably reduced relative to S1. We conclude that the globular, active site region of the myosin head is a stable, independently folded domain with intrinsic motor activity, but the coupling efficiency between ATP hydrolysis and movement declines markedly as the light chain binding region is truncated.

PHOELIX: a package for semi-automated helical reconstruction

We describe a set of procedures and algorithms which have been developed to provide an efficient and reliable method for reconstructing a three-dimensional density map from specimens with helical symmetry. These procedures build on the original MRC helical processing suite, with extensions principally developed using the SUPRIM image processing package. Actomyosin is used as a model specimen to demonstrate the utility of this repackaged and expanded set of routines. The time required to complete a three-dimensional map has been reduced from several weeks using traditional manual techniques to a few days. The increased signal/noise provided has allowed for the extraction of additional layer lines not previously identified by manual techniques.

Electron diffraction of helical particles

The development of low-dose electron cryo-microscopy has provided the means to see structural details to better than 10 A resolution in helical structures. The application of techniques of image analysis to micrographs can yield accurate phases, but not amplitudes with which to generate three-dimensional maps of the structure. Electron diffraction can provide reliable amplitudes, which can be combined with the phases from the images. In order to collect amplitude data, two problems have to be overcome: the pattern should be obtained from a large well ordered sample of particles, and the inelastic background should be properly subtracted. In this paper, we present three simple methods to produce rafts of helical particles. Using these methods we have obtained electron diffraction patterns from TMV (with data out to 0.28 nm), TMV protein stacked disks (with data out to 0.3 nm) and bacterial flagellar filaments (with data out to 0.5 nm). In addition, we describe the algorithms used to extract the amplitudes from the diffraction patterns.

A 13-A map of the actin-scruin filament from the limulus acrosomal process

We have determined the structure of the actin-scruin filament to 13-A resolution using a combination of low-dose EM and image analysis. The three-dimensional map reveals four actin-actin contacts: two within each strand and two between strands. The conformation of the actin subunit is different from that in the Holmes et al. (1990) model as refined by Lorenz et al. (1993). In particular, subdomain II is tilted in a similar way to that seen by Orlova and Egelman (1993) in F-Mg2(+)-ADP actin filaments in the absence of Ca2+. Scruin appears to consist of two domains of approximately equal volume. Each scruin subunit cross-links the two strands in the actin filament. Domain I of scruin contacts subdomain I of actin and makes a second contact at the junction of subdomains III and IV. Domain II of scruin contacts actin at subdomains I and II of a neighboring actin subunit. The two scruin domains thus bind differently to actin.

Electron crystallography of macromolecules

Numerous technical advances in electron crystallography have facilitated determination of the three-dimensional structures of macromolecules, especially those that form two-dimensional or helical periodic arrays. Several recent studies have demonstrated the utility of this technique for visualizing secondary structure such as alpha-helices and beta-sheets of membrane proteins and, in one case, the entire polypeptide backbone. Electron crystallography, therefore, has great potential as a tool for studying structural problems that are relevant to both molecular biology and biotechnology.

Teaching electron diffraction and imaging of macromolecules

Electron microscopic analysis can be used to determine the three-dimensional structures of macromolecules at resolutions ranging between 3 and 30 A. It differs from nuclear magnetic resonance spectroscopy or x-ray crystallography in that it allows an object's Coulomb potential functions to be determined directly from images and can be used to study relatively complex macromolecular assemblies in a crystalline or noncrystalline state. Electron imaging already has provided valuable structural information about various biological systems, including membrane proteins, protein-nucleic acid complexes, contractile and motile protein assemblies, viruses, and transport complexes for ions or macromolecules. This article, organized as a series of lectures, presents the biophysical principles of three-dimensional analysis of objects possessing different symmetries.

Size of the export channel in the flagellar filament of Salmonella typhimurium

The size of the putative export channel in the bacterial flagellar filament appears small (25 A) in studies done by electron microscopy but large (60 A) in studies done by X-ray diffraction. We have undertaken additional studies by electron microscopy to examine some of the possible causes of the difference. A comparison of three-dimensional image reconstructions of native and reconstituted filaments rules out the presence or absence of flagellin monomers in the export channel as the source of the variation in apparent channel size. The channel seen in reconstructions from both kinds of filaments is 25 A in diameter. The difference in the previous studies is more probably a result of artifacts introduced in either the X-ray or the electron microscopical methodology. Comparisons of three-dimensional reconstructions from images of filaments embedded in various stains (anionic, cationic and neutral) and in ice, taken at a range of defocuses, rule out the two most likely sources of artifact in electron microscopy (i.e., staining artifacts and defocus phase contrast). Based on these studies we suggest that the channel seen in the image reconstructions is free of exported flagellin monomers, that its true diameter is about 25 A, and, therefore, that the flagellin monomer must be unfolded to pass along it.