Three-dimensional structure of bovine pancreatic DNase I at 2.5 A resolution

The three-dimensional structure of bovine pancreatic deoxyribonuclease I (DNase I) has been determined at 2.5 A resolution by X-ray diffraction from single crystals. An atomic model was fitted into the electron density using a graphics display system. DNase I is an alpha, beta-protein with two 6-stranded beta-pleated sheets packed against each other forming the core of a 'sandwich'-type structure. The two predominantly anti-parallel beta-sheets are flanked by three longer alpha-helices and extensive loop regions. The carbohydrate side chain attached to Asn 18 is protruding by approximately 15 A from the otherwise compact molecule of approximate dimensions 45 A X 40 A. The binding site of CA2+-deoxythymidine-3',5'-biphosphate (Ca-pdTp) has been determined by difference Fourier techniques confirming biochemical results that the active centre is close to His 131. Ca-pdTp binds at the surface of the enzyme between the two beta-pleated sheets and seems to interact with several charged amino acid side chains. Active site geometry and folding pattern of DNase I are quite different from staphylococcal nuclease, the only other Ca2+-dependent deoxyribonuclease whose structure is known at high resolution. The electron density map indicates that two Ca2+ ions are bound to the enzyme under crystallization conditions.     

Crystallographic studies of the chicken gizzard G-actin X DNase I complex at 5A resolution

The structure of the chicken gizzard G-actin X DNase I complex has been determined at 5 A resolution by an X-ray diffraction method. Protein phases were computed by the multiple isomorphous replacement method using four heavy atom derivatives. The mean figure of merit was 0.65. Dimensions of the three molecular species, the complex, G-actin and DNase I, were determined based on the "cypress wood" models derived from the electron density map. The natures of the heavy atom binding sites are discussed in relation to the distinction between the two component molecules. The pattern of successive contacts between actin molecules observed in the present crystal seems unrelated to that found in F-actin.     

The low-resolution structure of human muscle aldolase

The three-dimensional structure of human muscle aldolase has been solved at 5 A resolution with the use of two isomorphous heavy atom derivatives. The enzyme's four subunits are arranged about three mutually perpendicular intersecting twofold axes to form a compact spherical molecule. The subunit boundaries are clearly defined but a possible domain structure is not apparent in this preliminary electron density map.     

Low-resolution structure refinement in electron microscopy

A real-space structure refinement method, originally developed for macromolecular X-ray crystallography, has been applied to protein structure analysis by electron microscopy (EM). This method simultaneously optimizes the fit of an atomic model to a density map and the stereo-chemical properties of the model by minimizing an energy function. The performance of this method is characterized at different resolution and signal-to-noise ratio conditions typical for EM electron density maps. A multi-resolution scheme is devised to improve the convergence of the refinement on the global energy minimum. Applications of the method to various model systems are demonstrated here. The first case is the arrangement of FlgE molecules in the helical filament of flagellar hook, in which refinement with segmented rigid bodies improves the density correlation and reduces severe van der Waals contacts among the symmetry-related subunits. The second case is a conformational analysis of the NSF AAA ATPase in which a multi-conformer model is used in the refinement to investigate the arrangement of the two ATPase domains in the molecule. The third case is a docking simulation in which the crystal structure of actin and the NOE data from NMR experiments on the dematin headpiece are combined with a low-resolution EM density map to generate an atomic model of the F-actin-dematin headpiece structure.     

Localization of the yeast RNA polymerase I-specific subunits

The spatial distribution of four subunits specifically associated to the yeast DNA-dependent RNA polymerase I (RNA pol I) was studied by electron microscopy. A structural model of the native enzyme was determined by cryo-electron microscopy from isolated molecules and was compared with the atomic structure of RNA pol II Delta 4/7, which lacks the specific polypeptides. The two models were aligned and a difference map revealed four additional protein densities present in RNA pol I, which were characterized by immunolabelling. A protruding protein density named stalk was found to contain the RNA pol I-specific subunits A43 and A14. The docking with the atomic structure showed that the stalk protruded from the structure at the same site as the C-terminal domain (CTD) of the largest subunit of RNA pol II. Subunit A49 was placed on top of the clamp whereas subunit A34.5 bound at the entrance of the DNA binding cleft, where it could contact the downstream DNA. The location of the RNA pol I-specific subunits is correlated with their biological activity.     

Three-dimensional reconstruction of an actin bundle

We present the three-dimensional structure of an actin filament bundle from the sperm of Limulus. The bundle is a motile structure which by changing its twist, converts from a coiled to an extended form. The bundle is composed of actin plus two auxiliary proteins of molecular masses 50 and 60 kD. Fraying the bundle with potassium thiocyanate created three classes of filaments: actin, actin plus the 60-kD protein, and actin plus both the auxiliary proteins. We examined these filaments by transmission electron microscopy and scanning transmission electron microscopy (STEM). Three-dimensional reconstructions from electron micrographs allowed us to visualize the actin subunit and the 60- and 50-kD subunits bound to it. The actin subunit appears to be bilobed with dimensions 70 X 40 X 35 A. The inner lobe of the actin subunit, located at 20 A radius, is a prolate ellipsoid, 50 X 25 A; the outer actin lobe, at 30 A radius, is a 35-A-diam spheroid. Attached to the inner lobe of actin is the 60-kD protein, an oblate spheroid, 55 X 40 A, at 50 A radius. The armlike 50-kD protein, at 55 A radius, links the 60-kD protein on one of actin's twin strands to the outer lobe of the actin subunit on the opposite strand. We speculate that the 60-kD protein may be a bundling protein and that the 50-kD protein may be responsible for the change in twist of the filaments which causes extension of the bundle.     

Low resolution structure of human erythrocyte glutathione reductase

Glutathione reductase from human erythrocytes is a dimeric flavoenzyme with a molecular weight of 100,000. X-ray diffraction analysis using the isomorphous replacement technique with four heavy-atom derivatives yielded an electron density map at 6 Å resolution with a figure of merit of 0.88. Only minor cuts had to be made in the electron density map to isolate one molecule. The dimer interface is on a crystallographic 2-fold axis. Each subunit can be subdivided into three domains: I, II and III, which are aggregated in such a way that deep clefts are formed on opposite sides of the subunit. These clefts accommodate the substrate glutathione, binding to domain III, and the oxidized cofactor NADP, binding to domain I in a similar extended conformation as NAD binds to the dehydrogenases. The shortest connection between the centres of the nicotinamide ring of NADP and the cystine of oxidized glutathione is 18 Å long and goes along the interface between domains II and III right through the centre of the subunit. Presumably, FAD binds to domain II and its isoalloxazine ring bridges the gap between NADP and glutathione.     

Protein interfaces and intersubunit bonding. The case of tomato bushy stunt virus.

An atomic model of the subunit of tomato bushy stunt virus (TBSV) has been constructed to fit an electron density map at 2.9 A resolution. Subunit interfaces show networks of polar residues forming H-bonds and salt bridges. The way in which alternative specific bonding geometries are built into a contact are described.     

The molecular structure of insecticyanin from the tobacco hornworm Manduca sexta L. at 2.6 A resolution.

Insecticyanin, a blue biliprotein isolated from the tobacco hornworm Manduca sexta L., is involved in insect camouflage. Its three-dimensional structure has now been solved to 2.6 A resolution using the techniques of multiple isomorphous replacement, non-crystallographic symmetry averaging about a local 2-fold rotation axis and solvent flattening. All 189 amino acids have been fitted to the electron density map. The map clearly shows that insecticyanin is a tetramer with one of its molecular 2-fold axes coincident to a crystallographic dyad. The individual subunits have overall dimensions of 44 A X 37 A X 40 A and consist primarily of an eight-stranded anti-parallel beta-barrel flanked on one side by a 4.5-turn alpha-helix. Interestingly the overall three-dimensional fold of the insecticyanin subunit shows remarkable similarity to the structural motifs of bovine beta-lactoglobulin and the human serum retinol-binding protein. The electron density attributable to the chromophore is unambiguous and shows that it is indeed the gamma-isomer of biliverdin. The biliverdin lies towards the open end of the beta-barrel with its two propionate side chains pointing towards the solvent and it adopts a rather folded conformation, much like a heme.     

Structural relationships of actin, myosin, and tropomyosin revealed by cryo-electron microscopy

We have calculated three-dimensional maps from images of myosin subfragment-1 (S1)-decorated thin filaments and S1-decorated actin filaments preserved in frozen solution. By averaging many data sets we obtained highly reproducible maps that can be interpreted simply to provide a model for the native structure of decorated filaments. From our results we have made the following conclusions. The bulk of the actin monomer is approximately 65 X 40 X 40 A and is composed of two domains. In the filaments the monomers are strongly connected along the genetic helix with weaker connections following the long pitch helix. The long axis of the monomer lies roughly perpendicular to the filament axis. The myosin head (S1) approaches the actin filament tangentially and binds to a single actin, the major interaction being with the outermost domain of actin. In the map the longest chord of S1 is approximately 130 A. The region of S1 closest to actin is of high density, whereas the part furthest away is poorly defined and may be disordered. By comparing maps from decorated thin filaments with those from decorated actin, we demonstrate that tropomyosin is bound to the inner domain of actin just in front of the myosin binding site at a radius of approximately 40 A. A small change in the azimuthal position of tropomyosin, as has been suggested by others to occur during Ca2+-mediated regulation in vertebrate striated muscle, appears to be insufficient to eclipse totally the major site of interaction between actin and myosin.     

Preliminary crystal structure of Acinetobacter glutaminasificans glutaminase-asparaginase

The preliminary structure of a glutaminase-asparaginase from Acinetobacter glutaminasificans is reported. The structure was determined at 3.0-A resolution with a combination of phase information from multiple isomorphous replacement at 4-5-A resolution and phase improvement and extension by two density modification techniques. The electron density map was fitted by a polypeptide chain that was initially polyalanine. This was subsequently replaced by a polypeptide with an amino acid sequence in agreement with the sizes and shapes of the side chain electron densities. The crystallographic R factor is 0.300 following restrained least squares refinement with data to 2.9-A resolution. The A. glutaminasificans glutaminase-asparaginase subunit folds into two domains: the aminoterminal domain contains a five-stranded beta sheet surrounded by five alpha helices, while the carboxyl-terminal domain contains three alpha helices and less regular structure. The connectivity is not fully determined at present, due in part to the lack of a complete amino acid sequence. The A. glutaminasificans glutaminase-asparaginase structure has been used successfully to determine the relative orientations of the molecules in crystals of Pseudomonas 7A glutaminase-asparaginase, in crystals of Vibrio succinogenes asparaginase, and in a new crystal form of Escherichia coli asparaginase (space group 1222, one subunit per asymmetric unit).     

Structure of the yeast vacuolar ATPase

The subunit architecture of the yeast vacuolar ATPase (V-ATPase) was analyzed by single particle transmission electron microscopy and electrospray ionization (ESI) tandem mass spectrometry. A three-dimensional model of the intact V-ATPase was calculated from two-dimensional projections of the complex at a resolution of 25 angstroms. Images of yeast V-ATPase decorated with monoclonal antibodies against subunits A, E, and G position subunit A within the pseudo-hexagonal arrangement in the V1, the N terminus of subunit G in the V1-V0 interface, and the C terminus of subunit E at the top of the V1 domain. ESI tandem mass spectrometry of yeast V1-ATPase showed that subunits E and G are most easily lost in collision-induced dissociation, consistent with a peripheral location of the subunits. An atomic model of the yeast V-ATPase was generated by fitting of the available x-ray crystal structures into the electron microscopy-derived electron density map. The resulting atomic model of the yeast vacuolar ATPase serves as a framework to help understand the role the peripheral stalk subunits are playing in the regulation of the ATP hydrolysis driven proton pumping activity of the vacuolar ATPase.     

Three-dimensional structure of p-cresol methylhydroxylase (flavocytochrome c) from Pseudomonas putida at 3.0-A resolution.

p-Cresol methylhydroxylase (PCMH) isolated from Pseudomonas putida is an alpha 2 beta 2 tetramer of approximate subunit Mr 49,000 and 9,000. It is a flavocytochrome c containing covalently bound FAD in the larger subunit and covalently bound heme in the smaller. Crystals in space group P2(1)2(1)2(1) with unit-cell parameters a = 140.3 A, b = 130.6 A, and c = 74.1 A contain one full molecule per asymmetric unit and diffract anisotropically to about 2.8-A resolution in two directions and to about 3.3-A resolution in the third. An electron density map has been computed at a nominal resolution of 3.0 A by use of area detector data from native crystals and from two derivatives. The phases were improved with the B.C. Wang solvent leveling procedure, and the map was averaged about the noncrystallographic 2-fold axis. The cytochrome subunit, whose amino acid sequence is known, has been fitted to the electron density on a graphics system. The course of the polypeptide chain of the flavoprotein subunit, whose sequence is mostly unknown, has been traced in a minimap and a model of polyalanine fitted to the electron density on the graphics system. The flavoprotein subunit consists of three domains in close contact. The N-terminal domain consists largely of beta-structure and contains most of the FAD binding site. The second domain contains a seven-stranded antiparallel beta-sheet of unusual topology connected by antiparallel alpha-helices on one side. The flavin ring lies at the juncture of the first two domains. The third domain lies against the first domain and helps cover the rest of the FAD chain. The cytochrome subunit resembles other small cytochromes such as c-551 and c5 and fits into a depression on the surface of the large flavoprotein subunit. The flavin and heme planes are nearly perpendicular, the normals to the planes being approximately 65 degrees apart. The two groups are separated by about 8 A, the distance from one of the vinyl methylene carbon atoms of the heme to the 8 alpha-methyl group of the flavin ring.     

Crystal structure of muconate lactonizing enzyme at 6.5 A resolution

We have obtained crystals of Pseudomonas putida muconate lactonizing enzyme. They diffract to better than 2.4 A resolution and have two monomers in the asymmetric unit, related by a non-crystallographic 2-fold axis. The cell dimensions are 139.3 A X 139.3 A X 84.1 A, and the space group is I4. The electron density map at 6.5 A resolution shows that the enzyme is an octamer with D4 symmetry.     

Structure of yeast hexokinase. II. A 6 angstrom resolution electron density map showing molecular shape and heterologous interaction of subunits

An electron density map of yeast hexokinase has been calculated at 6 Å resolution using six heavy atom derivatives. The map shows each of the enzyme's two 51,000 molecular weight subunits to consist of two separate lobes connected by a narrow bridge of density. Furthermore, these two subunits are related to each other in the asymmetric unit of the crystal by a quasi-2-fold rather than a true 2-fold axis. That is, they are related by a rotation of 180 ° plus a relative translation of 3.6 Å along the symmetry axis. This gives rise to a heterologous subunit interaction and a possibility of non-identical structure and function for these chemically identical subunits. The molecule is quite asymmetric, having dimensions of 150 Å × 45 Å × 55 Å. Each subunit is about 80 Å × 40 Å × 50 Å.A portion of an electron density map at 3 Å resolution has been also calculated, based on phases from two heavy atom derivatives. Polypeptide backbone and side chains are visible in this map.     

Association of deoxyribonuclease I with the pointed ends of actin filaments in human red blood cell membrane skeletons

We have characterized the interaction of bovine pancreatic deoxyribonuclease I (DNase I) with the filamentous (F-)actin of red cell membrane skeletons stabilized with phalloidin. The hydrolysis of [3H]DNA was used to assay DNase I. We found that DNase I bound to a homogenous class of approximately equal to 2.4 X 10(4) sites/skeleton with an association rate constant of approximately 1 X 10(6) M-1 S-1 and a KD of 1.9 X 10(-9) M at 20 degrees C. Phalloidin lowered the dissociation constant by approximately 1 order of magnitude. The DNase I which sedimented with the skeletons was catalytically inactive but could be reactivated by dissociation from the actin. Actin and DNA bound to DNase I in a mutually exclusive fashion without formation of a ternary complex. Phalloidin-treated red cell F-actin resembled rabbit muscle G-actin in all respects tested. Since the DNase I binding capacity of the skeletons corresponded to the number of actin protofilaments previously estimated by other methods, it seemed likely that the enzyme binding site was confined to one end of the filament. We confirmed this premise by showing that elongating the red cell filaments with rabbit muscle actin monomers did not appreciably add to their capacity to bind or inhibit DNase I. Saturation of skeletons with cytochalasin D or gelsolin, avid ligands for the barbed end of actin filaments, did not reduce their binding of DNase I. Furthermore, neither cytochalasin D nor DNase I alone blocked all of the sites for addition of monomeric pyrene-labeled rabbit muscle G-actin to phalloidin-treated skeletons; however, a combination of the two agents did so. In the presence of phalloidin, the polymerization of 300 nM pyrenyl actin on nuclei constructed from 5 nM gelsolin and 25 nM rabbit muscle G-actin was completely inhibited by 35 nM DNase I but not by 35 nM cytochalasin D. We conclude that DNase I associates uniquely with and caps the pointed (slow-growing or negative) end of F-actin. These results imply that the amino-terminal, DNase I-binding domain of the actin protomer is oriented toward the pointed end and is buried along the length of the actin filament.     

Cryo-EM Structure of the Yeast ATP Synthase

We have used electron cryomicroscopy of single particles to determine the structure of the ATP synthase from Saccharomyces cerevisiae. The resulting map at 24 Å resolution can accommodate atomic models of the F₁-c₁₀ subcomplex, the peripheral stalk subcomplex, and the N-terminal domain of the oligomycin sensitivity conferral protein. The map is similar to an earlier electron cryomicroscopy structure of bovine mitochondrial ATP synthase but with important differences. It resolves the internal structure of the membrane region of the complex, especially the membrane embedded subunits b, c, and a. Comparison of the yeast ATP synthase map, which lacks density from the dimer-specific subunits e and g, with a map of the bovine enzyme that included e and g indicates where these subunits are located in the intact complex. This new map has allowed construction of a model of subunit arrangement in the F_O motor of ATP synthase that dictates how dimerization of the complex via subunits e and g might occur.     

Multiple subunit fitting into a low-resolution density map of a macromolecular complex using a gaussian mixture model

Recently, electron microscopy measurement of single particles has enabled us to reconstruct a low-resolution 3D density map of large biomolecular complexes. If structures of the complex subunits can be solved by x-ray crystallography at atomic resolution, fitting these models into the 3D density map can generate an atomic resolution model of the entire large complex. The fitting of multiple subunits, however, generally requires large computational costs; therefore, development of an efficient algorithm is required. We developed a fast fitting program, “gmfit”, which employs a Gaussian mixture model (GMM) to represent approximated shapes of the 3D density map and the atomic models. A GMM is a distribution function composed by adding together several 3D Gaussian density functions. Because our model analytically provides an integral of a product of two distribution functions, it enables us to quickly calculate the fitness of the density map and the atomic models. Using the integral, two types of potential energy function are introduced: the attraction potential energy between a 3D density map and each subunit, and the repulsion potential energy between subunits. The restraint energy for symmetry is also employed to build symmetrical origomeric complexes. To find the optimal configuration of subunits, we randomly generated initial configurations of subunit models, and performed a steepest-descent method using forces and torques of the three potential energies. Comparison between an original density map and its GMM showed that the required number of Gaussian distribution functions for a given accuracy depended on both resolution and molecular size. We then performed test fitting calculations for simulated low-resolution density maps of atomic models of homodimer, trimer, and hexamer, using different search parameters. The results indicated that our method was able to rebuild atomic models of a complex even for maps of 30 Å resolution if sufficient numbers (eight or more) of Gaussian distribution functions were employed for each subunit, and the symmetric restraints were assigned for complexes with more than three subunits. As a more realistic test, we tried to build an atomic model of the GroEL/ES complex by fitting 21-subunit atomic models into the 3D density map obtained by cryoelectron microscopy using the C7 symmetric restraints. A model with low root mean-square deviations (14.7 Å) was obtained as the lowest-energy model, showing that our fitting method was reasonably accurate. Inclusion of other restraints from biological and biochemical experiments could further enhance the accuracy.     

Atomic structures at last: the ribosome in 2000

Last year, atomic structures of the 50S ribosomal subunit from Haloarcula marismortui and of the 30S ribosomal subunit from Thermus thermophilus were published. A year before that, a 7.8 A resolution electron density map of the 70S ribosome from T. thermophilus appeared. This information is revolutionizing our understanding of protein synthesis.     

Polylysine induces an antiparallel actin dimer that nucleates filament assembly: crystal structure at 3.5-A resolution

An antiparallel actin dimer has been proposed to be an intermediate species during actin filament nucleation. We now show that latrunculin A, a marine natural product that inhibits actin polymerization, arrests polylysine-induced nucleation at the level of an antiparallel dimer, resulting in its accumulation. These dimers, when composed of pyrene-labeled actin subunits, give rise to a fluorescent excimer, permitting detection during polymerization in vitro. We report the crystallographic structure of the polylysine-actin-latrunculin A complex at 3.5-A resolution. The non-crystallographic contact is consistent with a dimeric structure and confirms the antiparallel orientation of its subunits. The crystallographic contacts reveal that the mobile DNase I binding loop of one subunit of a symmetry-related antiparallel actin dimer is partially stabilized in the interface between the two subunits of a second antiparallel dimer. These results provide a potential explanation for the paradoxical nucleation of actin filaments that have exclusively parallel subunits by a dimer containing antiparallel subunits.