Three-dimensional reconstruction of the flagellar hook from Caulobacter crescentus

The structure of the bacterial flagellar hook produced by a mutant of Caulobacter crescentus was studied by electron microscopy, optical diffraction, and digital image processing techniques. The helical surface lattice of the hook is defined by a single, right-handed genetic helix having a pitch of about 23 Å, an axial rise per subunit of 4 Å and an azimuthal angle between subunits of 64·5 °. The lattice is also characterized by intersecting families of 5-start, 6-start and long-pitch 11-start helices. These helical parameters are remarkably similar to those determined for the flagellar filaments from several strains of gram-negative bacteria. The technique of three-dimensional image reconstruction (DeRosier & Klug, 1968) was applied to nine of the better preserved specimens and the diffraction data from five of these were correlated and averaged and used to generate an average three-dimensional model of the hook. The pattern of density modulations in the three-dimensional model is suggestive of an elongated, curved shape for the hook subunit (100 Å × 25 Å × 25 Å). The subunits are situated in the lattice of the polyhook such that their long axes are tilted about 45 ° with respect to the hook axis. The subunits appear to make contact with each other along the 6-start helices at a radius of 80 Å and also along the 11-start helices at a radius of 65 Å. Few structural features are revealed at radii between 15 å and 45 Å and, therefore, we are unable to decide to what extent the hook subunits extend into this region. The most striking characteristic of the model is the presence of deep, broad, continuous 6-start helical grooves extending from an inner radius of about 50 Å to the perimeter of the particle at 105 Å radius. Normal hooks usually appear curved in electron micrographs and sometimes so are the mutant hooks; the prominent 6-start grooves appear to allow for bending with minimal distortion of matter in the outer regions of the hook. A round stain-filled channel about 25 Å in diameter runs down the center of the polyhook. Such a channel supports a model for flagellar assembly in which flagellin subunits travel through the interior of the flagellum to the growing distal end of the filament.     

Caulobacter crescentus bacteriophage phiCbK: structure and in vitro self-assembly of the tail

Electron micrographs of negatively stained and platinum-shadowed bacteriophage φCbK have been analyzed by optical diffraction and computer Fourier transformation. The results show that the phage tail is a helical “stacked disc” structure with an annular repeat of about 38 Å and with 3-fold rotational symmetry about the helix axis. Phage tails exhibited lateral and rotational flexibility and were found to possess variable helical parameters. The smaller angle of rotation about the helix axis between equivalent asymmetric units on adjacent discs measured from a number of tail images was found to have an average value of 41.5±0.9 °. Cross-sectional views of short tail fragments were obtained after sonication at 0 °C. These views confirmed the 3-fold symmetry of the 38 Å annular unit, which most probably consists of three identical subunits of the major tail protein. Formation of extended tail polymers, both linear and circular, was found to take place spontaneously in vitro after sonication. On the basis of these results, a low-resolution model for the tail helix is presented. The questions of head-tail symmetry mismatch in the phage and of tail length regulation are discussed.     

Structure of actin filament bundles from microvilli of sea urchin eggs

The detailed substructure of actin filament bundles in microvilli of fertilized sea urchin eggs has been studied by analysing electron microscope images of negatively stained specimens. Transverse stripes which repeat about every 130 Å along the axis of a bundle, as previously observed by Burgess & Schroeder (1977), reflect the positions of cross-bridges that connect the filaments into a bundle. Analysis of optical transforms of the micrographs reveals that there are approximately 14 actin monomers between cross-overs of the two long-pitch helical strands of the actin filaments, with three cross-bridges in this interval. The structure is basically similar to that of the hexagonally packed bundles prepared in vitro from high speed supernatants of sea urchin eggs by Kane (1975) and analyzed by DeRosier et al. (1977). One clear difference, however, is that the in vivo microvillar filament bundles are supercoiled, giving rise to long axial repeats of 1500 to 2000 Å.Computationally filtered images of regions that were only slightly supercoiled reveal the relative alignment of filaments within the bundles and show that crossbridges appear to interact with four actin monomers, apparently linking two actin monomers on one strand of one filament to the nearest two monomers on a neighbouring filament. However, the cross-bridges are not spaced at equal intervals corresponding to four actin subunits, presumably because of the lack of hexagonal symmetry in the individual filaments, which have about 14 actin monomers between cross-overs. Instead, the cross-bridges are arranged quasiequivalently along the longitudinal axis of the bundles, in steps of four or five actin subunit spacings (28 Å each).     

Characterization of crystals of a cytochrome oxidase (nitrite reductase) from Pseudomonas aeruginosa by x-ray diffraction and electron microscopy

Cytochrome oxidase from Pseudomonas aeruginosa has been crystallized from 2 m-ammonium sulfate. The crystals occur principally as thin diamond-shaped plates of space group P2₁2₁2 with unit cell dimensions of 92 Å × 115 Å × 76 Å. Determination of the density of glutaraldehyde-fixed, water-equilibrated crystals (1.167 g/cm³), coupled with the unit cell volume (804,000 ų), indicates that there is one subunit (~63,000 Mr) per asymmetric unit. X-ray diffraction data which were limited to 12 Å resolution due to small crystal size were obtained for the hk0 and 0kl zones using precession photography. Amplitude and phase data for the hk0, 0kl, and h0l zones were obtained from computer-based Fourier analysis of appropriate micrographs recorded from negatively stained microplates and thin sections of larger crystals using minimal beam electron microscopy. For crystals embedded in the presence of tannic acid it was possible to achieve 20 Å resolution which is comparable to the resolution achieved with negative staining of thin crystalline arrays. In addition, unstained electron diffraction on glutaraldehyde-fixed, glucose-stabilized plates was recorded to a resolution of 9 Å. The three-dimensional packing of the cytochrome oxidase dimer in the unit cell has been deduced from computer reconstructed images of the three principal projections along the crystallographic axes. The cytochrome oxidase dimer is located in the unit cell with the dimer axis coincident with a crystallographic 2-fold axis; thus within the resolution of the present data in projection (9 Å) the two subunits are identical, in agreement with biochemical evidence. The crystals have been prepared with the enzyme in the fully oxidized state and upon reduction a progressive cracking of the crystals is observed, possibly due to a conformational change dependent on the oxidation state of the heme iron.     

Architecture of the Chinese hamster metaphase chromosome

The development of procedures for the isolation of unfixed metaphase chromosomes has made feasible a direct analysis of their morphology. Wholemount stereo electron microscopy was used to examine intact and partially disrupted chromosomes produced by physical shearing and extraction with salt and urea solutions. A model of chromosome architecture was developed to accommodate evidence from studies using both light and electron microscopy. In the proposed model the chromatid (anaphase chromosome) consists of two half-chromatids; each half-chromatid contains two deoxyribonucleoprotein ribbons wound into a single fiber (termed the core), with many loops of chromatin (termed epichromatin) attached along its length. The core ribbons are each about 50 Å thick by 4000 Å wide and are composed of many parallel deoxyribonucleoprotein strands. The epichromatin loops appear to be 250 Å supercoiled fibers containing about 75 per cent of the chromosomal DNA. The epichromatin can be selectively removed from the core fibers by extraction with 2.0 M NaCl or 6.0 M urea solutions.     

Structure of Limulus telson muscle thick filaments

Computer analysis of electron micrographs of negatively stained thick filaments isolated from the telson levator muscle of the horseshoe crab (Limulus polyphemus) has shown that they have a four-stranded helical structure. The repeating units along each helix have a bent extended shape (measuring approximately 20 nm × 8 nm × 8 nm) and are inclined at an angle of about 30 ° to the helical path. At the resolution of this study, it was difficult to establish the exact size of the surface subunits, but our results are probably more consistent with each unit representing the two heads of a single myosin molecule rather than larger aggregates.     

Assembly in vitro of bacteriophage P22 procapsids from purified coat and scaffolding subunits

The coat and scaffolding proteins of bacteriophage P22 procapsids have been purified in soluble form. By incubating both purified proteins with a mutant-infected cell extract lacking procapsids, but competent for DNA packaging in vitro (Poteete et al., 1979), we were able to obtain assembly of biologically active procapsids in vitro. The active species for complementation in vitro in both protein preparations copurified with the soluble subunits, indicating that these subunits represent precursors in procapsid polymerization.When the purified coat and scaffolding subunits were mixed directly, they polymerized into double-shelled procapsid-like structures during dialysis from 1.5 m-guanidine hydrochloride to buffer. When dialyzed separately under the same conditions, the scaffolding subunits did not polymerize but remained as soluble subunits, as did most of the coat subunits. No evidence was found for self-assembly of the scaffolding protein in the absence of the coat protein.The unassembled coat subunits sedimented at 3.9 S and the unassembled scaffolding subunits sedimented at 2.4 S in sucrose gradients. The Stokes' radius, determined by gel filtration, was 25 Å for the coat subunits and 34 Å for the scaffolding subunits. These results indicate that the scaffolding subunits are relatively slender elongated molecules, whereas the coat subunits are more globular.The experiments suggest that the procapsid is built by copolymerization of the two protein species. Their interaction on the growing surface of the shell structure, and not in solution, appears to regulate successive binding interactions.     

X-ray diffraction and electron microscope studies on the structure of bacterial F pili.

F pili are hollow cylinders with 80 Å outer diameter and 20 Å inner diameter. Both X-ray fibre diffraction and optical diffraction of electron micrographs show a strong layer-line corresponding to a spacing of 32 Å, to which a J₄ Bessel function is assigned on the basis of the optical diffraction. X-ray diffraction patterns show near-meridional intensity on a layer-line corresponding to a spacing of 12.8 Å, to which a J₁ Bessel function is assigned. Mass per length measurements on unstained specimens in the scanning transmission electron microscope give 3000 daltons/Å, indicating that the 11,200 dalton pilin subunits are 3.7 Å apart along the axial direction of the pili. These observations show that the pilus structure can be represented as four coaxial helices of pitch 128 Å with the pilin subunits elongated and overlapping along the line of these helices. Each of these helices of subunits is translated axially with respect to its neighbour, to give a basic helix of 3.6 units per turn of 12.8 Å pitch. Radial electron density calculations indicate a 50 Å diameter girdle of hydrophobic amino acids between the inner and outer diameters of the protein shell. A molecular model of the structure at low resolution is presented.     

Flagellar hook structures of Caulobacter and Salmonella and their relationship to filament structure

Native flagellar hooks from a polarly flagellated bacterium, Caulobacter crescentus, and polyhooks from a peritrichously flagellated bacterium, Salmonella typhimurium. have been studied by densitometry of electron micrographs of negatively stained specimens, followed by computerized Fourier analysis and three-dimensional reconstruction. The two structures are remarkably similar. In both cases, the subunits are arranged along a right-handed basic helix of 2.3 nm pitch with successive subunits separated by an azimuthal angle of 64 to 65 °, and there is a pronounced system of continuous 6-start grooves and ridges on the surface of the structures. The subunit of Salmonella (M_r 42,000, versus 70,000 for Caulobacter) is somewhat thinner and yields a smaller overall hook diameter. The “bent finger” subunit shape and orientation in both cases suggests that the hook could bend readily by a sliding motion in the 11-start direction at inner radii, with the 6-start groove preventing collision at outer radii. The basic helical pitch of the Salmonella hook structure, and the number of subunits per basic helical turn (5.56) makes it highly compatible with the Salmonella flagellar filament (2.6 nm pitch. 5.51 subunits per turn); so also does the elongated shape and tilt angle of the hook and flagellin subunits in the respective structures. The two structures may therefore conjoin directly in the intact flagellum, although participation of a minor protein is not ruled out by the data.     

The growth of ordered two-dimensional sheets of ribosomal particles from salt-alcohol mixtures

A procedure for the in vitro growth of well-ordered two-dimensional sheets from ribosomal particles using salts and salt-alcohol mixtures has been developed. Employing this procedure, ordered two-dimensional sheets of the wild type as well as of mutated 50 S ribosomal subunits from Bacillus stearothermophilus can readily be obtained. These sheets, stained with uranyl acetate or gold-thioglucose, are suitable for three-dimensional image reconstruction. They consist of relatively small unit cells with dimensions of 160 +/- 15 and 365 +/- 20 A. Diffraction patterns of electron micrographs of these sheets contain features to 25 A resolution.     

Evidence for a mixed lattice in microtubules reassembled in vitro

An extensive structural analysis of microtubules assembled in vitro has been carried out using electron microscopy in conjunction with computer analysis based on Fourier transforms and helical diffraction theory. Microtubules assembled in vitro displayed a range of numbers of protofilaments from 12 to 16, with 14 the most abundant (84% in one large sampling). In almost all structures observed protofilaments are staggered to form a characteristic 3-start shallow helix. The presence of the 3-start helix was confirmed by fiber tilting experiments to correct the effects of microtubule flattening. Since α and β tubulin subunits alternate along the protofilaments, continuous helical lattices can be constructed with interactions between adjacent protofilaments involving unlike subunits (type A lattice) or like subunits (type B lattice). However, the 14-protofilament, 3-start microtubules are incompatible with either the A or B-type continuous helical lattice. Evidence is presented which indicates that lattice discontinuities are present which generate features of both the A and B-types, with the latter predominating.     

Molecular structure determination by electron microscopy of unstained crystalline specimens.

The projected structures of two unstained periodic biological specimens, the purple membrane and catalase, have been determined by electron microscopy to resolutions of 7 Å and 9 Å, respectively. Glucose was used to facilitate their in vacuo preservation and extremely low electron doses were applied to avoid their destruction.The information on which the projections are based was extracted from defocussed bright-field micrographs and electron diffraction patterns. Fourier analysis of the micrograph data provided the phases of the Fourier components of the structures; measurement of the electron diffraction patterns provided the amplitudes.Large regions of the micrographs (3000 to 10,000 unit cells) were required for each analysis because of the inherently low image contrast (<1%) and the statistical noise due to the low electron dose.Our methods appear to be limited in resolution only by the performance of the microscope at the unusually low magnifications which were necessary. Resolutions close to 3 Å should ultimately be possible.     

Characterization and crystallization of ribosomal particles from Halobacterium marismortui

Ribosomes and their subunits have been isolated from Halobacterium marismortui, an extremely halophilic bacterium from the Dead Sea. The stability and functional activity of the subunits were tested under a wide range of salt conditions. Three-dimensional microcrystals of the large ribosomal subunits have been obtained. Electron microscopy of positively stained thin sections of these crystals showed that the particles are closely packed with approximate cell constants of 310 × 350 Å.     

Small protein B interacts with the large and the small subunits of a stalled ribosome during trans-translation

During trans-translation, stalled bacterial ribosomes are rescued by small protein B (SmpB) and by transfer-messenger RNA (tmRNA). Stalled ribosomes switch translation from the defective messages to a short internal reading frame on tmRNA that tags the nascent peptide chain for degradation and recycles the ribosomes. We present evidences that SmpB binds the large and small ribosomal subunits in vivo and in vitro. The binding between SmpB and the ribosomal subunits is very tight, with a dissociation constant of 1.7 × 10⁻¹⁰ M, similar to its K_D for the 70S ribosome or for tmRNA. tmRNA displaces SmpB from its 50S binding but not from the 30S. In vivo, SmpB is detected on the 50S when trans-translation is impaired by lacking tmRNA or a functional SmpB. SmpB contacts the large subunit transiently and early during the trans-translational process. The affinity of SmpB for the two ribosomal subunits is modulated by tmRNA in the course of trans-translation. It is the first example of two copies of the same protein interacting with two different functional sites of the ribosomes.     

Structure of polar pili from Pseudomonas aeruginosa strains K and O

The polar pili of Pseudomonas aeruginosa strains K and O are hollow cylinders with 52 Å outer diameter and 12 Å inner diameter. There is a girdle of low electron density (interpreted as due to a local concentration of hydrophobic amino acid side-chains) centred at 31 Å diameter. Similar X-ray diffraction patterns are obtained from oriented fibres of the two types of pili, to a resolution of 7 Å in the equatorial direction and 4 Å in the meridional direction. The two types of pilin protein subunits have a similar molecular weight, and their sequences contain a number of homologous regions. They form a helical array with 4.06 to 4.08 units per turn of a basic helix that has a pitch of 40.8 Å for strain K pili and 41.3 Å for strain O pili at 75% relative humidity. A method is described for distinguishing between very similar diffraction patterns.There is strong intensity at 10 Å near the equator and at 5 Å near the meridian on the diffraction patterns. This intensity distribution is characteristic of α-helical rods running roughly in the direction of the fibre axis. The orientation of these rods was established by the fit between the transform of an α-helical polyalanine model and the strong near-equatorial layer-line.     

Extra-long bacteriophage T4 tails produced under in vitro conditions

Extra-long bacteriophage T4 tails have been produced under in vitro conditions from purified tails of normal length. These tails show a range of lengths suggesting that the basic increment of increased length is the 41 Å (Moody, 1971) axial repeating unit rather than the length of a normal tail. Some extra-long tails and tubes attached to baseplates show stain penetration down the central tunnel of the tube to approximately the normal tail length. The stain-penetrated tunnel, as visualised by three-dimensional reconstruction from the electron micrographs, has a diameter between 30 and 40 Å, sufficient to allow the passage of DNA. The exclusion of stain from the tunnel in the baseplate-near segment of the tube is interpreted as being due to the presence of additional material in the tunnel. The relevance of these observations to the assembly and length-regulation of the tail is discussed.     

Structure of the tubulin dimer in zinc-induced sheets

The structure of tubulin has been studied in projection by minimum beam electron microscopy and image processing of negatively stained zinc-induced sheets. The reconstructed images include data to 15 Å resolution.We report here a clear and reproducible 82 Å repeat arising from the arrangement of heterodimers in sheet aggregates of tubulin. This repeat is only observed in diffraction patterns from images recorded by minimum beam methods (10 to 20 e/Ų) and arises from small, but consistent, structural differences between two similar subunits believed to represent the two chemical species of tubulin monomer (M_r, 55,000). At higher electron doses (100 to 200 e/Ų), the additional information is lost or very much reduced, and only a repeat of 41 Å is observed, owing to the loss of distinction between monomers in the tubulin heterodimer.The sheets are composed of 49 Å wide, polar protofilaments, similar to those observed in microtubules; however, the interprotofilament packing is completely different in the two structures. In these sheets, adjacent protofilaments point and face in opposite directions; i.e. they are related by dyad-screw axes normal to the protofilament axes and in the plane of the sheet. Thus, the zinc-induced sheets are crystals of space group P2₁, with cell dimensions of about 97 Å × 82 Å, containing one tubulin heterodimer per asymmetric unit.Reconstructed images of four individual sheets, and their average, show the arrangement and shapes of the two heterodimers contained in each unit cell. The structure and packing of heterodimers in sheets are compared to those in opened out microtubules where all protofilaments point and face in the same direction.     

The suitability of a monofunctional reagent of an undecagold cluster for phasing data collected from the large ribosomal subunits from Bacillus stearothermophilus

An electron density map of the large ribosomal subunit from Bacillus stearothermophilus was obtained at 26 Å resolution by single isomorphous replacement (SIR) from a derivative formed by specific quantitative labeling with a dense undecagold cluster. For derivalization, a mono-functional reagent of this cluster was bound to a sulfhydryl group of a purified ribosomal protein. which was in turn reconstituted with core particles of a mutant lacking this protein. The native, mutated, and derivatzed 50S ribosomal subunits crystallize under the same conditions in the same space group. Under favorable conditions, crystals of the derivatized subunit proved to be isomorphous with the native ones, whereas the crystals of the mutant may have somewhat different packing. After resolving the SIR phase ambiguity by solvent flattening, the electron density shows a packing that is consistent with the noncrystallographic symmetry found by Patterson searches as well as with the motif observed in electron micrographs of thin sections of the crystals. These studies established that phase information can be obtained from heavy metal clusters, even when the crystals under investigation are unstable and weakly diffracting. These results encouraged further effort at the construction of specifically derivatized crystals from other ribosomal particles that diffract to higher resolution. © 1994 John Wiley & Sons, Inc.     

In vitro polymerization of bacteriophage T4D tail core subunits

The in vitro polymerization of bacteriophage T4 core protein subunits (P19) onto baseplates is examined by electron microscopy. Procedures for purifying P19 and baseplates, both of which have in vitro complementation activity, are described. It is found that when P19 and baseplates are allowed to react over a wide range of initial concentration ratios, the most probable core length is about 1000 Å, the length found in vivo. Very few structures longer than this are observed if the polymerization is not allowed to proceed for much longer than one hour. Some physical properties of the baseplates were determined. These are s_20,W= 72 S, D_20,W = 8.56 × 10^?8 cm²/s, andM_r = 7.4 ± 0.3 × 10⁶.     

Collagen polymorphism: its origins in the amino acid sequence.

The polymorphic forms of ordered collagen aggregation in vitro and in vivo are reviewed. The axially projected structures of a class of fibrils known as fibrous long spacing (FLS) collagen are solved using simulated positively stained banding patterns based on the amino acid sequence. This method is also used to solve the axial projection of a 670 Å (D) periodic structure with a symmetrical banding pattern (DPS) re-precipitated from skin collagen. The relation between the obliquely striated and 110 Å periodic forms of collagen is discussed. The specificity for the formation of FLS, DPS and segment long spacing (SLS) collagen is shown to be in the distributions of various amino acids in the sequence. Different residues are important for each type of structure, their importance being dependent on the chemical conditions and the presence of other macromolecules. The interaction of collagen fibrils with proteoglycans in vivo is discussed in terms of the amino acid sequence. Also the factors which affect collagen morphology in the presence of mucopolysaccharides and proteoglycans in vitro and in vivo are discussed. Some insight is gamed into the principles which govern the self-assembly of molecules into ordered fibrous aggregates.