Three-dimensional reconstruction of single particles embedded in ice

Cryo-electron microscopy of GDP-tubulin rings

Rings of guanosine diphosphate (GDP)-tubulin formed in the presence of divalent cations have been studied using conventional negative stain and cryo-electron microscopy. The structure of such rings resembles that of depolymerizing microtubule ends and corresponds to an "unconstrained" conformation of tubulin in its GDP state. The use of cryo-techniques has allowed us to image the ring polymers free from dehydration and flattening artifacts. Preparations of frozen-hydrated GDP-tubulin rings are generally heterogeneous and contain a mixture of double, triple, and incomplete rings, as well as spirals and some rare single rings. Images of different polymer types can be identified and classified into groups that are then amenable for averaging and single particle reconstruction methods. Identifying the differences in tubulin structure, between straight and curve protofilaments, will be important to understand the molecular bases of dynamic instability in microtubules.

The tripartite type III secreton of Shigella flexneri inserts IpaB and IpaC into host membranes

Bacterial type III secretion systems serve to translocate proteins into eukaryotic cells, requiring a secreton and a translocator for proteins to pass the bacterial and host membranes. We used the contact hemolytic activity of Shigella flexneri to investigate its putative translocator. Hemolysis was caused by formation of a 25-A pore within the red blood cell (RBC) membrane. Of the five proteins secreted by Shigella upon activation of its type III secretion system, only the hydrophobic IpaB and IpaC were tightly associated with RBC membranes isolated after hemolysis. Ipa protein secretion and hemolysis were kinetically coupled processes. However, Ipa protein secretion in the immediate vicinity of RBCs was not sufficient to cause hemolysis in the absence of centrifugation. Centrifugation reduced the distance between bacterial and RBC membranes beyond a critical threshold. Electron microscopy analysis indicated that secretons were constitutively assembled at 37 degrees C before any host contact. They were composed of three parts: (a) an external needle, (b) a neck domain, and (c) a large proximal bulb. Secreton morphology did not change upon activation of secretion. In mutants of some genes encoding the secretion machinery the organelle was absent, whereas ipaB and ipaC mutants displayed normal secretons.

Mitochondrial localization and oligomeric structure of HClpP, the human homologue of E. coli ClpP

A bacterially expressed recombinant HClpP protein, the human homologue of Escherichia coli ClpP protease, was used to obtain specific polyclonal antibodies. Those antibodies identify a 26 kDa polypeptide in mitochondrial subcellular fractions of rat and human liver. Immunofluorescence and electron microscopic studies demonstrate that the mammalian homologue of ClpP is located in the mitochondrial matrix with a tendency to be found in association with the inner mitochondrial membrane. An HClpP recombinant protein with a truncated NH2terminus (missing the first 58 amino acid residues) shows a molecular mass of 26 kDa under denaturing conditions. This N-truncated HClpP recombinant protein shows a native molecular mass of 340 kDa that is identical with the native molecular mass of the partially purified protein from rat liver mitochondria. Electron microscopy shows that the N-truncated recombinant HClpP has a ring shape with seven identical morphological units in the periphery, exhibiting a 7-fold symmetry. The native molecular mass and the electron microscopic studies suggest that mitochondrial ClpP is composed of two heptameric rings with 7-fold symmetry, similar to E. coli ClpP.

Structural comparison of cephalopod hemocyanins: phylogenetic significance

Hemocyanins, the respiratory molecules of cephalopod mollusks, are hollow cylinders with five internal arches. Three hemocyanins representative of three orders of cephalopods (Benthoctopus species, Octopoda; Vampyroteuthis infernalis, Vampyromorpha; Sepia officinalis, Sepioidea) were subjected to cryoelectron microscopy and three-dimensional (3D) reconstruction. The structure of Benthoctopus hemocyanin, solved at 26.4-A resolution, possesses arches comprising two identical functional units. The similarity between these functional units and the structure recently observed in X-ray crystallography for Octopus by Cuff et al. (J. Mol. Biol., 1998, 232, 522-529) allows the identification of their N- and C-terminal domains in the 3D reconstruction volume. Conversely, arches present in the 3D reconstruction volume of Sepia hemocyanin (21.8 A resolution) contain four functional units that are disposed differently. The strong resemblance between the reconstruction volumes of Vampyroteuthis (21.4-A resolution) and Benthoctopus hemocyanins suggests that Sepioidea diverged from a group containing Octopoda and Vampyromorpha.

Oligomeric structures of the phage phi29 histone-like protein p6

Protein p6 of Bacillus subtilis phage phi29 has been described as a histone-like protein, playing a role in genome organization and compaction, on the basis of its high intracellular abundance, its pleiotropic effect, and its ability to bind and highly compact the whole phi29 DNA in vitro. Protein p6 forms large multimeric nucleoprotein complexes in which a right-handed superhelical DNA wraps toroidally around the protein core. Analytical ultracentrifugation analysis, at the concentration estimated in vivo (at least 1 mM), showed that protein p6 self-associates into elongated oligomers, suggesting that, in the absence of DNA, the protein could form a scaffold for DNA binding. In this work we have studied the structure of these oligomers by transmission electron microscopy and image processing. The results show that protein p6 aggregates into crooked-shaped oligomers, compatible with a helical structure. The oligomers could interact head-to-tail to form doughnut-shaped structures or they could grow into right-handed double-helical filaments by a nucleation-dependent polymerization process. The dimensions of the crooked-shaped structures are in agreement with that of the DNA in the nucleoprotein complex previously described. We propose that the crooked-shaped structures could act as a scaffold imposing the right-handed path followed by the DNA, and thus it could be considered a non-transient DNA chaperone.

Human Dmc1 protein binds DNA as an octameric ring

The bacterial RecA protein has been the most intensively studied enzyme in homologous genetic recombination. The core of RecA is structurally homologous to that of the F1-ATPase and helicases. Like the F1-ATPase and ring helicases, RecA forms a hexameric ring. The human Dmc1 (hDmc1) protein, a meiosis-specific recombinase, is homologous to RecA. We show that hDmc1 forms octameric rings. Unlike RecA and Rad51, however, hDmc1 protein does not form helical filaments. The hDmc1 ring binds DNA in the central channel, as do the ring helicases, which is likely to represent the active form of the protein. These observations indicate that the conservation of the RecA-like ring structure extends from bacteria to humans, and that some RecA homologs may form both rings and filaments, whereas others may function only as rings.

Three-dimensional structure of herpes simplex virus type 1 glycoprotein D at 2.4-nanometer resolution

Herpes simplex virus type 1 glycoprotein D (gD) is essential for virus infectivity and is responsible for binding to cellular membrane proteins and subsequently promoting fusion between the virus envelope and the cell. No structural data are available for gD or for any other herpesvirus envelope protein. Here we present a three-dimensional model for the baculovirus-expressed truncated protein gD1(306t) based on electron microscopic data. We demonstrate that gD1(306t) appears as a homotetramer containing a pronounced pocket in the center of the molecule. Monoclonal antibody binding demonstrates that the molecule is oriented such that the pocket protrudes away from the virus envelope.

A two-exposure technique for ice-embedded samples successfully reconstructs the chlorocruorin pigment of Sabella spallanzanii at 2. 1 Nm resolution

A technique for reconstructing ice-embedded macromolecules from electron micrographs taken at two specimen tilts (+/-23 degrees ) has been used to determine the structure of chlorocruorin isolated from the Polychaete annelid Sabella spallanzanii. Images of individual molecules were extracted in couples from two micrographs of the same field of view so each couple consists of two projections of the same molecule. One couple was used as a fixed reference for alignment. Different references yielded reconstructions with different orientations. These were merged to give a model against which the orientation of 1624 first-exposure images was refined to give a final reconstruction at 2.1 nm resolution. The structure of this hematic pigment, essentially the same as that for Lumbricus terrestris, is a bilayer structure with overall symmetry D6, containing six hollow groups per layer. A hollow group is formed by six globular masses and has approximate threefold symmetry. Other structural elements connect the two layers and the hollow groups in a layer. This non-globin material occupies about 15% of the total molecular volume. The results show that the double-exposure strategy, previously described by some of the authors and tested in computer simulations, performs well in real experiments and could be used to obtain preliminary reconstructions in a semiautomatic way.

The reaction center complex from the green sulfur bacterium Chlorobium tepidum: a structural analysis by scanning transmission electron microscopy

The three-dimensional (3D) structure of the reaction center (RC) complex isolated from the green sulfur bacterium Chlorobium tepidum was determined from projections of negatively stained preparations by angular reconstitution. The purified complex contained the PscA, PscC, PscB, PscD subunits and the Fenna-Matthews-Olson (FMO) protein. Its mass was found to be 454 kDa by scanning transmission electron microscopy (STEM), indicating the presence of two copies of the PscA subunit, one copy of the PscB and PscD subunits, three FMO proteins and at least one copy of the PscC subunit. An additional mass peak at 183 kDa suggested that FMO trimers copurify with the RC complexes. Images of negatively stained RC complexes were recorded by STEM and aligned and classified by multivariate statistical analysis. Averages of the major classes indicated that different morphologies of the elongated particles (length=19 nm, width=8 nm) resulted from a rotation around the long axis. The 3D map reconstructed from these projections allowed visualization of the RC complex associated with one FMO trimer. A second FMO trimer could be correspondingly accommodated to yield a symmetric complex, a structure observed in a small number of side views and proposed to be the intact form of the RC complex.

3D imaging of the 58 kDa cell binding subunit of the Helicobacter pylori cytotoxin

Pathogenic strains of Helicobacter pylori produce a potent exotoxin, VacA, which intoxicates gastric epithelial cells and leads to peptic ulcer. The toxin is released from the bacteria as a high molecular mass homo-oligomer of a 95 kDa polypeptide which undergoes specific proteolytic cleavage to 37 kDa and 58 kDa subunits. We have engineered a strain of H. pylori to delete the gene sequence coding for the 37 kDa subunit. The remaining 58 kDa subunit is expressed efficiently and exported as a soluble dimer that is non-toxic but binds target cells in a manner similar to the holotoxin. A 3D reconstruction of the molecule from electron micrographs of quick-freeze, deep-etched preparations reveals the contribution of each building block to the structure and permits the reconstruction of the oligomeric holotoxin starting from individual subunits. In this model P58 subunits are assembled in a ring structure with P37 subunits laying on the top. The data indicate that the 58 kDa subunit is capable of folding autonomously into a discrete structure recognizable within the holotoxin and containing the cell binding domain.

Three-dimensional reconstruction of Lumbricus terrestris hemoglobin at 22 A resolution: intramolecular localization of the globin and linker chains

A 3D reconstruction of the hemoglobin (Hb) of the earthworm Lumbricus terrestris was carried out by the 3D projection alignment method from electron microscopy images of a frozen-hydrated specimen at 22 A resolution. The results were analyzed by a new approach taking into account the evolution of the 210 densities forming the 3D volume as a function of the threshold of surface representation. The whole oligomer with D6point-group symmetry is comprised of 12 hollow globular substructures (HGS) with local 3-fold symmetry tethered to a complex network of linking subunits (linker complex). The 12 globin subunits of each HGS are distributed around local 3-fold axis in four layers of three subunits. The first layer, the most external, contains monomeric globin chains 2A, 3A, and 5A. The three trimers corresponding to the nine remaining subunits have one subunit in each of the second (2B, 3B, 5B), third (1A, 4A, 6A), and fourth (1B, 4B, 6B) layer. The distances between the centers of the globin chains forming the trimers are in the ranges 20-32 A and 45-52 A. The linker complex is made up of two types of linking units. The first type forms three loops connecting globin chains of the second, third and fourth layers. The average molecular mass (Mm) of these subunits was 25 kDa. The second type forms the central structure, termed hexagonal toroid, and its 12 connections to the HGS. This structure corresponds to a hexamer of a single linking unit with a Mm (31.2 kDa), size and a shape different from those of the HGS loops. A careful study of 3D volume architecture shows that each toroid linking unit is bound to the three loops of a HGS pair located in the upper and lower hexagonal layers, respectively. As shown in a model of architecture, hexagonal bilayered (HBL) Hbs can be built very simply from 144 globin chains and 42 linker chains belonging to two different types. We also propose a simple assembly sequence for the construction of HBL Hbs based on the architecture model.

Mitochondrial Lon of Saccharomyces cerevisiae is a ring-shaped protease with seven flexible subunits

Lon (or La) is a soluble, homooligomeric ATP-dependent protease. Mass determination and cryoelectron microscopy of pure mitochondrial Lon from Saccharomyces cerevisiae identify Lon as a flexible ring-shaped heptamer. In the presence of ATP or 5'-adenylylimidodiphosphate, most of the rings are symmetric and resemble other ATP-driven machines that mediate folding and degradation of proteins. In the absence of nucleotides, most of the rings are distorted, with two adjacent subunits forming leg-like protrusions. These results suggest that asymmetric conformational changes serve to power processive unfolding and translocation of substrates to the active site of the Lon protease.

Domain architecture of the bacteriophage phi29 connector protein

Viral connectors are essential components of the DNA packaging machinery. They interact with nucleic acids and other viral components to translocate DNA inside the viral head. We have attempted to locate the different structural and functional domains of the phage Phi29 connector using a combination of approaches to generate different antigenic probes. Complexes of native connectors with either monoclonal or monospecific antibodies were studied by immunoelectron microscopy and image averaging methods. The data were merged in a model of the connector domain structure at 2-3 nm resolution. This epitope mapping provides a general outline of the folding architecture of the connector polypeptide, following a complicated threading that places the amino and carboxyl-terminals in close alignment in the narrower domain at 2-3 nm from the top of the connector. The appendages are built up by a long and highly immunogenic sequence (amino acid residues 153 to 206). The RNA binding domain forms part of the top of the narrow conical area of the connector, a flexible region that undergoes structural changes during viral morphogenesis. The DNA binding domain is located not far away, 2-3 nm below, in the outer side of the narrow conical part. The precise location of the functional domains of the connector, as well as their relative positions provide the first experimental framework for understanding the connector function.

Rings and filaments of beta protein from bacteriophage lambda suggest a superfamily of recombination proteins

The beta protein of bacteriophage lambda acts in homologous genetic recombination by catalyzing the annealing of complementary single-stranded DNA produced by the lambda exonuclease. It has been shown that the beta protein binds to the products of the annealing reaction more tightly than to the initial substrates. We find that beta protein exists in three structural states. In the absence of DNA, beta protein forms inactive rings with approximately 12 subunits. The active form of the beta protein in the presence of oligonucleotides or single-stranded DNA is a ring, composed of approximately 15-18 subunits. The double-stranded products of the annealing reaction catalyzed by the rings are bound by beta protein in a left-handed helical structure, which protects the products from nucleolytic degradation. These observations suggest structural homology for a family of proteins, including the phage P22 erf, the bacterial RecT, and the eukaryotic Rad52 proteins, all of which are involved in homologous recombination.

Selection of antibody probes to correlate protein sequence domains with their structural distribution

We propose a new approach that permits correlation of specific domains defined by their primary sequence with their location in the structure of complex macromolecular aggregates. It is based on the combination of well-established structural analysis methods that incorporate the use of overlapping peptides on cellulose membranes for the isolation and purification of specific antibodies from a polyclonal antiserum. Monospecific antibodies to the connector protein of bacteriophage phi29 were isolated from polyclonal antisera using a new development of the spotscan method. These antibodies can be purified in quantities that allow antigenicity testing in enzyme-linked immunosorbent assays, Western blotting and immunoprecipitations, demonstrating the specificity of this isolation procedure. This approach has allowed us to generate direct antibody probes for immunoelectron microscopy mapping of different connector protein domains in a low resolution three-dimensional epitope map.

Structural details of proteinase entrapment by human alpha2-macroglobulin emerge from three-dimensional reconstructions of Fab labeled native, half-transformed, and transformed molecules

Three-dimensional electron microscopy reconstructions of native, half-transformed, and transformed alpha2-macroglobulins (alpha2Ms) labeled with a monoclonal Fab Fab offer new insight into the mechanism of its proteinase entrapment. Each alpha2M binds four Fabs, two at either end of its dimeric protomers approximately 145 A apart. In the native structure, the epitopes are near the base of its two chisel-like features, laterally separated by 120 A, whereas in the methylamine-transformed alpha2M, the epitopes are at the base of its four arms, laterally separated by 160 A. Upon thiol ester cleavage, the chisels on the native alpha2M appear to split with a separation and rotation to give the four arm-like extensions on transformed alpha2M. Thus, the receptor binding domains previously enclosed within the chisels are exposed. The labeled structures further indicate that the two protomeric strands that constitute the native and transformed molecules are related and reside one on each side of the major axes of these structures. The half-transformed structure shows that the two Fabs at one end of the molecule have an arrangement similar to those on the native alpha2M, whereas on its transformed end, they have rotated. The rotation is associated with a partial untwisting of the strands and an enlargement of the openings to the cavity. We propose that the enlarged openings permit the entrance of the proteinase. Then cleavage of the remaining bait domains by a second proteinase occurs with its entrance into the cavity. This is followed by a retwisting of the strands to encapsulate the proteinases and expose the receptor binding domains associated with the transformed alpha2M.

Biochemical and electron microscopic image analysis of the hexameric E1 helicase

DNA replication initiator proteins bind site specifically to origin sites and in most cases participate in the early steps of unwinding the duplex. The papillomavirus preinitiation complex that assembles on the origin of replication is composed of proteins E1 and the activator protein E2. E2 is an ancillary factor that increases the affinity of E1 for the ori site through cooperative binding. Here we show that duplex DNA affects E1 (in the absence of E2) to assemble into an active hexameric structure. As a 10-base oligonucleotide can also induce this oligomerization, it seems likely that DNA binding allosterically induces a conformation that enhances hexamers. E1 assembles as a bi-lobed, presumably double hexameric structure on duplex DNA and can initiate bi-directional unwinding from an ori site. The DNA takes an apparent straight path through the double hexamers. Image analysis of E1 hexameric rings shows that the structures are heterogeneous and have either a 6- or 3-fold symmetry. The rings are about 40-50 A thick and 125 A in diameter. The density of the central cavity appears to be a variable and we speculate that a plugged center may represent a conformational flexibility of a subdomain of the monomer, to date unreported for other hexameric helicases.

The ribosome-structure and functional ligand-binding experiments using cryo-electron microscopy

Cryo-electron microscopy has greatly advanced our understanding of the basic steps of protein synthesis in the bacterial ribosome. This article gives an overview of what has been achieved so far. Through three-dimensional visualization of complexes that represent the ribosome in defined binding states, locations were derived for the tRNA in A, P, and E sites, as well as the elongation factors. In addition, the pathways of messenger RNA and the exiting polypeptide chain could be inferred.

GroEL under heat-shock. Switching from a folding to a storing function

Chaperonin GroEL from Escherichia coli, together with its cochaperonin GroES, are proteins involved in assisting the folding of polypeptides. GroEL is a tetradecamer composed of two heptameric rings, which enclose a cavity where folding takes place through multiple cycles of substrate and GroES binding and release. GroEL and GroES are also heat-shock proteins, their synthesis being increased during heat-shock conditions to help the cell coping with the thermal stress. Our results suggest that, as the temperature increases, GroEL decreases its protein folding activity and starts acting as a "protein store." The molecular basis of this behavior is the loss of inter-ring signaling, which slows down GroES liberation from GroEL and therefore the release of the unfolded protein from the GroEL cavity. This behavior is reversible, and after heat-shock, GroEL reverts to its normal function. This might have a physiological meaning, since under thermal stress conditions, it may be inefficient for the cell to fold thermounstable proteins that are prone to denaturation.

Polymorphic quaternary organization of the Bacillus subtilis bacteriophage SPP1 replicative helicase (G40 P)

The Bacillus subtilis bacteriophage SPP1 gene 40 product (G40P), which belongs to the DnaB-like family of helicases, is essential for SPP1 genome replication. The active form of the enzyme is the hexamer, capable of DNA unwinding with a 5' to 3' polarity fueled by the hydrolysis of a nucleoside 5'-triphosphate. We have used electron microscopy of negatively stained G40P samples and image processing techniques to study the structural characteristics of the hexameric assemblies of this protein. Our results provide the first low resolution data on a hexameric helicase of a Gram-positive bacterial origin. A novel approach has been adopted to analyze possible symmetry heterogeneities, an unsupervised method based on a neural network self-organizing algorithm, which has led to the detection of different subclasses of G40P views. Two different quaternary states of G40P homohexamers sharing a C3 symmetry organization have been found, as well as a minor class that seems to reflect an alternative C6 symmetry architecture. These forms show general features known for other hexameric helicases, such as the ring-like arrangement of monomers around a central hole. A clear structural handedness has also been detected in some of these forms. An analysis of these quaternary states and a model for the structural organization of G40P are presented.

A maximum-likelihood approach to single-particle image refinement

The alignment of single-particle images fails at low signal-to-noise ratios and small particle sizes, because noise produces false peaks in the cross-correlation function used for alignment. A maximum-likelihood approach to the two-dimensional alignment problem is described which allows the underlying structure to be estimated from large data sets of very noisy images. Instead of finding the optimum alignment for each image, the algorithm forms a weighted sum over all possible in-plane rotations and translations of the image. The weighting factors, which are the probabilities of the image transformations, are computed as the exponential of a cross-correlation function. Simulated data sets were constructed and processed by the algorithm. The results demonstrate a greatly reduced sensitivity to the choice of a starting reference, and the ability to recover structures from large data sets having very low signal-to-noise ratios.

Are the light-harvesting I complexes from Rhodospirillum rubrum arranged around the reaction centre in a square geometry?

The basic photosynthetic unit containing the reaction centre and the light-harvesting I complex (RC-LHI) of the purple non-sulphur bacterium Rhodospirillum rubrum was purified and reconstituted into two-dimensional (2D) membrane crystals. Transmission electron microscopy using conventional techniques and cryoelectron microscopy of the purified single particles and of 2D crystals yielded a projection of the RC-LHI complex at a resolution of at least 1.6 nm. In this projection the LHI ring appears to have a square symmetry and packs in a square crystal lattice. The square geometry of the LHI ring was observed also in images of single isolated particles of the RC-LHI complex. However, although the LHI units are packed identically within the crystal lattice, a new rotational analysis developed here showed that the reaction centres take up one of four possible orientations within the ring. This fourfold disorder supports our interpretation of a square ring symmetry and suggests that a hitherto undetected component may be present within the photosynthetic unit.

Three-dimensional structure of the human plasmin alpha2-macroglobulin complex

The three-dimensional reconstructions of the human plasmin alpha2-macroglobulin binary complex were computed from electron microscopy images of stain and frozen-hydrated specimens. The structures show excellent agreement and reveal a molecule with approximate dimensions of 170 (length) x 140 (width) x 140 A (depth). The asymmetric plasmin structure imparts significant asymmetry to the plasmin alpha2-macroglobulin complex not seen in the structures resulting from the reaction of alpha2-macroglobulin with methylamine or chymotrypsin. The structure shows, when combined with other studies, that the C-terminal catalytic domain of the rod-shaped plasmin molecule is entrapped inside of the alpha2-macroglobulin cavity, whereas its N-terminal kringle domains protrude outside one end between the two arm-like features of the transformed alpha2-macroglobulin structure. This arrangement ensures that the catalytic site of plasmin is prevented from degrading plasma proteins. The internalized C-terminal portion of the plasmin structure resides primarily on the major axis of alpha2-macroglobulin, suggesting that after the initial cleavage of the two bait domains and the thiol esters, the rod-shaped plasmin molecule enters the alpha2-macroglobulin cavity through the large openings afforded by the half-transformed structure. This mode of entrapment requires the untwisting and the separation of the two strands that constitute the alpha2-macroglobulin structure.

Mapping flexible protein domains at subnanometer resolution with the atomic force microscope

The mapping of flexible protein domains with the atomic force microscope is reviewed. Examples discussed are the bacteriorhodopsin from Halobacterium salinarum, the head-tail-connector from phage phi29, and the hexagonally packed intermediate layer from Deinococcus radiodurans which all were recorded in physiological buffer solution. All three proteins undergo reversible structural changes that are reflected in standard deviation maps calculated from aligned topographs of individual protein complexes. Depending on the lateral resolution (up to 0.8 nm) flexible surface regions can ultimately be correlated with individual polypeptide loops. In addition, multivariate statistical classification revealed the major conformations of the protein surface.

Structure and NTPase activity of the RNA-translocating protein (P4) of bacteriophage phi 6

The RNA polymerase complex of bacteriophage phi 6 comprises four proteins, P1, P2, P4 and P7, and forms the core of the virion. Protein P4 is a non-specific NTPase that provides the energy required for RNA translocation (packaging). Characterization of purified recombinant P4 shows that the protein assembles into stable hexamers in the presence of ADP and divalent cations. Image averaging of electron micrographs reveals this hexamer as a slightly skewed ring with outer and inner diameters of 12 and 2 nm, respectively. NTPase activity of P4 is associated only with the hexameric form. Ca2+ and Zn2+ and non-specific single-stranded RNA stimulate the NTPase activity, while Mg2+ acts as a non-competitive inhibitor, presumably via a separate Mg2+ binding site. Binding affinities of different nucleotide mono-, di- and triphosphates and non-hydrolyzable analogs indicate that the beta-phosphate moiety is required for substrate binding. A slight preference for binding of purine nucleotides is also observed. Analysis of P4 by CD and Raman spectroscopy indicates an alpha/beta subunit fold that is altered only slightly by hexamer assembly. Raman markers of P4 secondary and tertiary structures are also largely invariant to nucleotide exchange and hydrolysis, suggesting that the mechanisms of RNA translocation involves movement of subunits relative to one another rather than large scale changes in the alpha/beta subunit fold. The stoichiometry of P4 in the mature phi 6 virion is estimated as 120 copies. Because the recombinant P4 hexamers exhibit hydrodynamic and enzymatic properties that are identical to those of P4 oligomers released from native phi 6, we propose that P4 occurs as hexamers in the native viral core particle.

ATP binding induces large conformational changes in the apical and equatorial domains of the eukaryotic chaperonin containing TCP-1 complex

The chaperonin-containing TCP-1 complex (CCT) is a heteromeric particle composed of eight different subunits arranged in two back-to-back 8-fold pseudo-symmetric rings. The structural and functional implications of nucleotide binding to the CCT complex was addressed by electron microscopy and image processing. Whereas ADP binding to CCT does not reveal major conformational differences when compared with nucleotide-free CCT, ATP binding induces large conformational changes in the apical and equatorial domains, shifting the latter domains up to 40 degrees (with respect to the inter-ring plane) compared with 10 degrees for nucleotide-free CCT or ADP-CCT. This equatorial ATP-induced shift has no counterpart in GroEL, its prokaryotic homologue, which suggests differences in the folding mechanism for CCT.

Three-dimensional structure of bovine NADH:ubiquinone oxidoreductase (complex I) at 22 A in ice

NADH:ubiquinone oxidoreductase (complex I) is the first and largest complex in the electron transport chain of mitochondria. The bovine complex purified from cardiac muscle consists of at least 42 different subunits with a combined molecular mass of about 890 kDa. The three-dimensional structure of the complex was determined at 22 A from single particles embedded in vitrified ice using electron cryo-microscopy. The structure was calculated using a new program to align particles, to correct for the contrast transfer function of the microscope, and to carry out the three-dimensional reconstruction of the complex. The bovine complex has the overall L-shaped appearance found in earlier studies of the closely related complex I from Neurospora crassa, but it differs by having a thin stalk region linking the membrane-bound globular arm with the intrinsic membrane domain. Thus, the stalk which measures about 30 A in diameter is likely to contain part of the electron transfer pathway linking the NADH binding site in the globular arm with the ubiquinone binding site in the membrane domain. The globular domain of bovine complex I is significantly bigger than that of the N. crassa enzyme, suggesting that the apparent additional subunit complexity of the bovine enzyme is associated with the globular part.

On the structural changes of native human alpha2-macroglobulin upon proteinase entrapment. Three-dimensional structure of the half-transformed molecule

The reconstructions of an intermediate form of human alpha2-macroglobulin (half-transformed alpha2M) in which two of its four bait regions and thiol ester sites were cleaved by chymotrypsin bound to Sepharose were obtained by three-dimensional electron microscopy from stain and frozen-hydrated specimens. The structures show excellent agreement and reveal a structure with approximate dimensions of 195 (length) x 135 (width) and 130 A (depth) with an internal funnel-shaped cavity. The structure shows that a chisel-shaped body is connected to a broad base at the opposing end by four stands. Four approximately 45 A diameter large openings in the body of the structure result in a central cavity that is more accessible to the proteinase than those associated with the native or fully transformed structures. The dissimilarity in the shapes between the two ends of alpha2M half-transformed and the similarity between its chisel-shaped body and that of native alpha2M indicate that the chymotrypsin has cleaved both bait regions in the bottom-half of the structure. Consequently, its functional division lies on the minor axis. The structural organization is in accord with biochemical studies, which show that the half-transformed alpha2M migrates on native polyacrylamide gels at a rate intermediate to the native and fully transformed alpha2M and is capable of trapping 1 mol of proteinase. Even though its upper portion is similar to the native molecule, significant differences in their shapes are apparent and these differences may be related to its slower reaction with a proteinase than the native structure. These structural comparisons further support the view that the transformation of alpha2M involves an untwisting of its strands with an opening of the cavity for entrance of the proteinase and a retwisting of the strands around the proteinase resulting in its encapsulation.

Structural characterization of a dynein motor domain

Cytoplasmic dynein is a microtubule-based mechanochemical protein that plays an essential role in cell division, vesicle transport, and cytoplasmic membrane organization. As a molecular motor, dynein utilizes an ATP hydrolysis mechanism to bind and release microtubules and to undergo conformational changes that result in a net displacement towards the microtubule's minus end. To visualize structural features of this motor protein, we have begun to characterize the dynein head domain by electron microscopy and image processing. Transmission electron microscopy of negatively stained native dynein from Dictyostelium has been performed and images of the head domain have been aligned and analyzed with the software SPIDER. The resulting 2D averages show an oblong round shape composed of seven to eight globular domains or lobes that encircle a stain-filled area. A recombinant 380 kDa fragment of the dynein heavy chain encodes just the globular head domain; analysis of these particles reveals a high structural similarity with the native head domain. A prominent stalk can be seen in several projections of this fragment, suggesting a structure analogous to the B-link described for some axonemal dyneins. Single tilt pair images were used to compute low resolution 3D reconstructions of the dynein head domain. These show a flattened spheroidal shape of 13.5 nm in length with seven similar domains arranged in a ring. Slices through the reconstructions reveal a large central cavity. This is the first detailed description of the head domain structure for a dynein molecule. The presence of a central cavity and the outer globular features, along with its large size make dynein structurally distinct from either myosin or kinesin.

Visualization of a large conformation change of ribosomes in Escherichia coli cells starved for tryptophan or treated with kirromycin

Computer-aided electron tomography has been used to visualize ribosomes in Escherichia coli cells treated with kirromycin. This antibiotic stops bacterial growth by blocking the release of EF-Tu. GDP from the ribosome after GTP cleavage. Ribosomes in the kirromycin-treated cells are very compact, with the two subunits in close contact with each other. This closed structure is different from the open structure with spatially separated subunits that characterizes ribosomes in tryptophan-starved cells, giving deficiency for tryptophanyl.tRNA. A comparison of ribosomes in exponentially growing bacteria suggests that most ribosomes in an undefined working mode are in the closed conformation.

Effects of the inter-ring communication in GroEL structural and functional asymmetry

The chaperonin GroEL consists of a double-ring structure that assists protein folding in the presence of GroES and ATP. Recent studies suggest that the 7-mer ring is the functional unit where protein folding takes place. Nevertheless, both GroEL rings are required to complete the reaction cycle through signals transmitted between the two rings. Electron microscopy, image processing, and biochemical analysis of GroEL, a single-ring mutant (SR1) and a inter-ring communication affected mutant (A126V), in the presence of ATP and adenylyl imidodiphosphate, have allowed the identification of a conformational change in the apical domains that is strictly dependent on the communication between the two GroEL rings. It is deduced from these results that the binding of nucleotide to both GroEL rings generates, as a consequence of the inter-ring communication, a functionally and structurally asymmetric particle. This asymmetric particle has a ring with a small conformational change in its apical domains and high affinity toward unfolded substrate and GroES, and the other ring has a larger conformational change in its apical domains and lower affinity toward substrate and GroES.

Automated correlation and averaging of three-dimensional reconstructions obtained by electron tomography

We have developed a least-squares refinement procedure that in an automated way performs three-dimensional alignment and averaging of objects from multiple reconstructions. The computer implementation aligns the three-dimensional structures by a two-step procedure that maximizes the density overlap for all objects. First, an initial average density is built by successive incorporation of individual objects, after a global search for their optimal three-dimensional orientations. Second, the initial average is subsequently refined by excluding individual objects one at a time, realigning them with the reduced average containing all other objects and including them into the average again. The refinement is repeated until no further change of the average occurs. The resulting average model is therefore minimally biased by the order in which the individual reconstructions are incorporated into the average. The performance of the procedure was tested using a synthetic data set of randomly oriented objects with Poisson-distributed noise added. The program managed well to align and average the objects at the signal/noise ratio 1.0. The increase in signal/noise ratio was in all investigated cases almost equal to the expected square root of the number of objects. The program was also successfully tested on a set of authentic three-dimensional reconstructions from an in situ specimen containing Escherichia coli 70S ribosomes, where the immediate environment of the reconstructed objects may also contain variable amounts of other structures.

The RepA protein of plasmid RSF1010 is a replicative DNA helicase

The RepA protein of the mobilizable broad host range plasmid RSF1010 has a key function in its replication. RepA is one of the smallest known helicases. The protein forms a homohexamer of 29,896-Da subunits. A variety of methods were used to analyze the quaternary structure of RepA. Gel filtration and cross-linking experiments demonstrated the hexameric structure, which was confirmed by electron microscopy and image reconstruction. These results agree with recent data obtained from RepA crystals diffracting at 3.5-A resolution (Röleke, D., Hoier, H., Bartsch, C., Umbach, P., Scherzinger, E., Lurz, R., and Saenger, W. (1997) Acta Crystallogr. Sec. D 53, 213-216). The RepA helicase has 5' --> 3' polarity. As do most true replicative helicases, RepA prefers a tailed substrate with an unpaired 3'-tail mimicking a replication fork. Optimal unwinding activity was achieved at the remarkably low pH of 5.5. In the presence of Mg2+ (Mn2+) ions, the RepA activity is fueled by ATP, dATP, GTP, and dGTP and less efficiently by CTP and dCTP. UTP and dTTP are poor effectors. Nonhydrolyzable ATP analogues, ADP, and pyrophosphate inhibit the helicase activity, whereas inorganic phosphate does not. The presence of Escherichia coli single-stranded DNA-binding protein stimulates unwinding at physiological pH 2-3-fold, whereas the RSF1010 replicon-specific primase, RepB' protein, has no effect, either in the presence or in the absence of single-stranded DNA-binding protein.

Flexibility within myosin heads revealed by negative stain and single-particle analysis

Electron microscopy of negatively stained myosin has previously revealed three discrete regions within the heads of the molecule. However, despite a probable resolution of approximately 2 nm, it is difficult to discern directly consistent details within these regions. This is due to variability in both head conformation and in staining. In this study, we applied single-particle image processing and classified heads into homogeneous groups. The improved signal-to-noise ratio after averaging these groups reveals substantially improved detail. The image averages were compared to a model simulating negative staining of the atomic structure of subfragment-1 (S1). This shows that the three head regions correspond to the motor domain and the essential and regulatory light chains. The image averages were very similar to particular views of the S1 model. They also revealed considerable flexibility between the motor and regulatory domains, despite the molecules having been prepared in the absence of nucleotide. This flexibility probably results from rotation of the regulatory domain about the motor domain, where the relative movement of the regulatory light chain is up to 12 nm, and is most clearly illustrated in animated sequences (available at http://www.leeds.ac.uk/chb/muscle/myosinhead.htm l). The sharply curved conformation of the atomic model of S1 is seen only rarely in our data, with straighter heads being more typical.

Utility of Butvar support film and methylamine tungstate stain in three-dimensional electron microscopy: agreement between stain and frozen-hydrated reconstructions

A random conical tilt reconstruction of negatively stained Saccharomyces cerevisiae fatty acid synthase was used as a model to compute a three-dimensional reconstruction from untilted stain specimens of the molecules in multiple orientations using a three-dimensional projection alignment method. The resulting structure (24 A resolution) has a more uniform resolution than the initial structure and the handedness revealed in the random conical tilt method is preserved. In a similar approach, this model was used to compute a 21-A-resolution frozen-hydrated structure from untilted specimens of the molecules in multiple orientations. Even though the reconstructions are in close agreement, the stain structure appears to enhance the protein density associated with less robust features. These procedures significantly reduce the time and effort required to obtain a three-dimensional reconstruction from frozen-hydrated data with a resolution that is comparable to the best obtained by more laborious methods. The agreement between the stain and frozen-hydrated reconstructions affords convincing evidence concerning the validity of the structure and the information afforded by the two reconstructions significantly enhances the structural analysis of the molecule.

Structural and functional effects of PA700 and modulator protein on proteasomes

Control and targeting of the proteolytic activity of the major intracellular protease, the proteasome, is accomplished by various regulatory protein complexes that may form higher-order assemblies with the proteasome. An activator of proteolytic activity, PA700, has been shown to have an ATP-dependent stimulatory effect on the peptidase activities of the proteasome, and another protein factor, the modulator, further enhances the effect of PA700. Here we show that the addition of PA700 endows the proteasome with the ability to cleave ubiquitinated proteins, a property associated with the previously isolated 26 S form of the proteasome. The modulator further stimulates this specific activity, without having any such effect on the proteasome alone. Using electron microscopy, we show that addition of PA700 causes the appearance of protein "caps" at one or both ends of proteasomes, forming structures that are indistinguishable from 26 S proteasomes. Quantitation of the numbers of uncapped, singly capped and doubly capped complexes indicates cooperativity in the association of PA700 with the two ends of the proteasome. Addition of modulator protein makes no further structural modification that is detectable by electron microscopy, but does cause an increase in the number of capped complexes visible at subsaturating concentrations of PA700. Hence PA700 converts the proteasome both functionally and structurally to the 26 S form, and the modulator promotes this transformation, apparently without stable association with the resulting complex.

Three-dimensional reconstruction of native and reassembled Lumbricus terrestris extracellular hemoglobin. Localization of the monomeric globin chains

The approximately 3.5 MDa hexagonal bilayer (HBL) hemoglobin (Hb) of the earthworm Lumbricus terrestris is composed of monomers and disulfide-bonded trimers (T) of globin chains and of four types of heme-deficient linker chains (L). Cryoelectron microscopic images of native Hb and of HBL reassembled from the constituent subunits depleted in monomer subunit (HBL[T+L]) were subjected to three-dimensional reconstructions by the random conical tilt series method. Native Hb has an architecture very similar to those of other annelid and vestimentiferan Hbs, consisting of 12 hollow globular substructures (HGS). Each HGS is comprised of six dense masses, has a 3-fold symmetry, and is organized in two hexagonally symmetric layers, with the vertices of the upper layer rotated 16 degrees clockwise relative to those of the lower layer. The layers are tethered to a central linker complex, consisting of two bracelets of connections perpendicular to the 6-fold axis and a set of six vertical connections linked to a flat hexagonal mass. HBL[T+L] shared all these features with the native Hb, except for a large hole around the 3-fold symmetry axis in each HGS, indicating the probable location of the missing monomer subunit.

Six molecules of SV40 large T antigen assemble in a propeller-shaped particle around a channel

The large T antigen of simian virus 40 (SV40) is a multifunctional regulatory protein, responsible for both the control of viral infection and the required alterations of cellular processes. T antigen is the only viral protein required for viral DNA replication. It binds specifically to the viral origin and as a helicase unwinds the SV40 DNA bidirectionally. The functional complex is a double hexameric oligomer. In the absence of DNA, but in the presence of ATP or a non-hydrolyzable analog, T antigen assembles into hexamers, which are active as a helicase when a partially single-stranded (3') entry site exists on the substrate. We have used negative staining electron microscopy, single particle image processing and three-dimensional reconstruction with a new algebraic reconstruction techniques (ART) algorithm to study the structure of these hexameric particles in the presence of different nucleotide cofactors (ATP, ADP, and the non-hydrolyzable analogs ATPgammaS and AMP-PNP). In every case a strong 6-fold structure was found, with the six density maxima arranged in a ring-like particle around a channel, and a well-defined vorticity. Because these structural features have recently been found in other prokaryotic helicases, they seem to be strongly related to the activity of the protein, which suggests a general functional model conserved through evolution.

Structure of the multidrug resistance P-glycoprotein to 2.5 nm resolution determined by electron microscopy and image analysis

P-glycoprotein (P-gp) is a member of the ATP binding cassette superfamily of active transporters and can confer multidrug resistance on cells and tumors by pumping chemotherapeutic drugs from the cytoplasm. P-gp was purified from CHrB30 cells and retained the ability to bind substrates and hydrolyze ATP. Labeling of P-gp with lectin-gold particles suggested it is monomeric. An initial structure of purified P-gp was determined to 2.5 nm resolution by electron microscopy and single particle image analysis of both detergent-solubilized and lipid-reconstituted protein. The structure was further refined by three dimensional reconstructions from single particle images and by Fourier projection maps of small two-dimensional crystalline arrays (unit cell parameters: a, 14.2 nm; b, 18.5 nm; and gamma, 91.6 degrees ). When viewed from above the membrane plane the protein is toroidal, with 6-fold symmetry and a diameter of about 10 nm. There is a large central pore of about 5 nm in diameter, which is closed at the inner (cytoplasmic) face of the membrane, forming an aqueous chamber within the membrane. An opening from this chamber to the lipid phase is present. The projection of the protein perpendicular to the membrane is roughly rectangular with a maximum depth of 8 nm and two 3-nm lobes exposed at the cytoplasmic face of the membrane, likely to correspond to the nucleotide binding domains. This study provides the first experimental insight into the three-dimensional architecture of any ATP binding cassette transporter.

Three-dimensional reconstruction with contrast transfer function correction from energy-filtered cryoelectron micrographs: procedure and application to the 70S Escherichia coli ribosome

Cryoelectron microscopy provides the means of studying macromolecules in their native state. However, the contrast transfer function (CTF) makes the images and the three-dimensional (3D) maps derived from them difficult to interpret. We developed methods to determine the CTF from experimental data and to obtain a CTF-corrected 3D reconstruction. The CTF correction and 3D reconstruction accomplished in one step make it easy to combine different defocus data sets and decrease the error accumulation in the computation. These methods were applied to energy-filtered images of the 70S Escherichia coli ribosome, resulting in a distortion-free 3D map of the ribosome at 1/24.5 A-1 resolution, as determined by the differential phase residual resolution criterion.

The thermosome: alternating alpha and beta-subunits within the chaperonin of the archaeon Thermoplasma acidophilum

The thermosome of the archaeon Thermoplasma acidophilum is composed of two subunits, alpha and beta, which are arranged in two stacked, eight-membered rings. Electron cryo-microscopy in conjunction with image analysis revealed a 4-fold symmetry in the heterooligomeric alpha + beta thermosome isolated from Thermoplasma, but not in the homooligomeric alpha-only thermosome expressed in Escherichia coli. This indicates that alpha and beta-subunits alternate within the rings of the Thermoplasma thermosome rather than forming two different homooligomeric rings. In addition, a small subpopulation of 9-fold symmetric complexes was found among the recombinant alpha-only thermosomes, and a central mass most likely representing bound substrate molecules was observed in about half of the native and recombinant thermosome particles.

Three-dimensional reconstruction of Limulus polyphemus hemocyanin from cryoelectron microscopy

Hemocyanin (Hc) the respiratory pigment of the horseshoe crab Limulus polyphemus (Lp) is composed of 48 approximately 75 kDa copper-containing subunits arranged in eight hexameric groups. In this study, we used the random conical tilt series method to do a three-dimensional (3D) reconstruction of Lp Hc observed in vitreous ice. This approach allowed the unambiguous determination of the handedness of the molecule. Lp Hc contains two superimposed 4 x 6mer structures possessing the same structural features as the other 4 x 6meric Hcs, namely flip and flop views and a rocking effect. Moreover, 3D fitting of the X-ray structure of subunit LpII with the reconstruction volume shows that the intra4 x 6meric contacts described in arthropod Hcs also occur within Limulus Hc. The two half-molecules composing the 8 x 6mer have their flop faces in contact (flop/flop association), the main links being formed by subunits LpIV. Model building shows that the flop/flop association is the only possible arrangement which allows the assembly of the whole particle. The two alternate constructions (flip/flop and flip/flip) are forbidden because of steric hindrance.