The structure of southern bean mosaic virus at 22.5 a resolution

Reversible swelling of SBMV is associated with reversible disordering

The structures of the compact and swollen southern bean mosaic virus (SBMV) particles have been compared by X-ray diffraction and proton magnetic resonance (PMR). Small-angle X-ray scattering showed that removal of divalent cations at alkaline pH causes the particle diameter to increase from 289 Å in the native SBMV by 12% in solution and by 9% in microcrystals. The swelling is fully reversible upon re-addition of Ca²⁺ and Mg²⁺ ions, as shown by the X-ray patterns at 6 Å resolution and by the 270 MHz PMR spectra. Beyond 30 Å resolution, X-ray patterns from the compact SBMV in solution and in microcrystals show fine fringes of ∼1/225 Å⁻¹ width extending to 6 Å resolution, whereas patterns from the swollen SBMV in solution and in microcrystals show only broader fringes of ∼1/90 Å⁻¹ width, Model calculations demonstrate that the fine fringes from compact SBMV arise from regular packing of the protein subunits on the icosahedral surface lattice; the smearing of fine fringes in the swollen virus pattern can be simulated by uncorrelated displacements of pentamers and hexamers of protein subunits, with a standard deviation of 6 Å from their mean locations. The PMR spectrum of compact SBMV is poorly resolved, whereas PMR spectrum of swollen SBMV shows sharp resonances in the methyl proton region. The line-narrowing for a fraction of the aliphatic protons upon swelling cannot be accounted for by rotational relaxation of the particle of 6 × 10⁶ MW, but must be attributed to internal motion in small regions of the protein subunits.

Confessions of an icosahedral virus crystallographer

This is a personal history of my structural studies of icosahedral viruses that evolved from crystallographic studies, to hybrid methods with electron cryo-microscopy and image reconstruction (cryoEM) and then developed further by incorporating a variety of physical methods to augment the high resolution crystallographic studies. It is not meant to be comprehensive, even for my own work, but hopefully provides some perspective on the growth of our understanding of these remarkable biologic assemblies. The goal is to provide a historical perspective for those new to the field and to emphasize the limitations of any one method, even those that provide atomic resolution information about viruses.

Preliminary X-ray data analysis of crystalline hibiscus chlorotic ringspot virus

Hibiscus chlorotic ringspot virus (HCRSV) is a positive-sense monopartite single-stranded RNA virus that belongs to the Carmovirus genus of the Tombusviridae family, which includes carnation mottle virus (CarMV). The HCRSV virion has a 30 nm diameter icosahedral capsid with T = 3 quasi-symmetry containing 180 copies of a 38 kDa coat protein (CP) and encapsidates a full-length 3.9 kb genomic RNA. Authentic virus was harvested from infected host kenaf leaves and was purified by saturated ammonium sulfate precipitation, sucrose density-gradient centrifugation and anion-exchange chromatography. Virus crystals were grown in multiple conditions; one of the crystals diffracted to 3.2 A resolution and allowed the collection of a partial data set. The crystal belonged to space group R32, with unit-cell parameters a = b = 336.4, c = 798.5 A. Packing considerations and rotation-function analysis determined that there were three particles per unit cell, all of which have the same orientation and fixed positions, and resulted in tenfold noncrystallography symmetry for real-space averaging. The crystals used for the structure determination of southern bean mosaic virus (SBMV) have nearly identical characteristics. Together, these findings will greatly aid the high-resolution structure determination of HCRSV.

Southern bean mosaic virus-specific proteins are synthesized in an in vitro system supplemented with intact, treated virions

RNA encapsidated in icosahedral particles of southern bean mosaic virus (SBMV) can act as a template for protein synthesis in an mRNA-dependent rabbit reticulocyte cell-free translation system, following dialysis of virions against mildly alkaline buffers. Exposure of the SBMV RNA template occurs only after addition of virus particles to the translation system and appears not to involve complete disruption of the protective SBMV capsid.

Ab initio phasing of high-symmetry macromolecular complexes: successful phasing of authentic poliovirus data to 3.0 A resolution

A genetic algorithm-based computational method for the ab initio phasing of diffraction data from crystals of symmetric macromolecular structures, such as icosahedral viruses, has been implemented and applied to authentic data from the P1/Mahoney strain of poliovirus. Using only single-wavelength native diffraction data, the method is shown to be able to generate correct phases, and thus electron density, to 3.0 A resolution. Beginning with no advance knowledge of the shape of the virus and only approximate knowledge of its size, the method uses a genetic algorithm to determine coarse, low-resolution (here, 20.5 A) models of the virus that obey the known non-crystallographic symmetry (NCS) constraints. The best scoring of these models are subjected to refinement and NCS-averaging, with subsequent phase extension to high resolution (3.0 A). Initial difficulties in phase extension were overcome by measuring and including all low-resolution terms in the transform. With the low-resolution data included, the method was successful in generating essentially correct phases and electron density to 6.0 A in every one of ten trials from different models identified by the genetic algorithm. Retrospective analysis revealed that these correct high-resolution solutions converged from a range of significantly different low-resolution phase sets (average differences of 59.7 degrees below 24 A). This method represents an efficient way to determine phases for icosahedral viruses, and has the advantage of producing phases free from model bias. It is expected that the method can be extended to other protein systems with high NCS.

The refined crystal structure of cowpea mosaic virus at 2.8 A resolution

Comoviruses are a group of plant viruses in the picornavirus superfamily. The type member of comoviruses, cowpea mosaic virus (CPMV), was crystallized in the cubic space group I23, a = 317 A and the hexagonal space group P6(1)22, a = 451 A, c = 1038 A. Structures of three closely similar nucleoprotein particles were determined in the cubic form. The roughly 300-A capsid was similar to the picornavirus capsid displaying a pseudo T = 3 (P = 3) surface lattice. The three beta-sandwich domains adopt two orientations, one with the long axis radial and the other two with the long axes tangential in reference to the capsid sphere. T = 3 viruses display one or the other of these two orientations. The CPMV capsid was permeable to cesium ions, leading to a disturbance of the beta-annulus inside a channel-like structure, suggesting an ion channel. The hexagonal crystal form diffracted X rays to 3 A resolution, despite the large unit cell. The large ( approximately 200 A) solvent channels in the lattice allow exchange of CPMV cognate Fab fragments. As an initial step in the structure determination of the CPMV/Fab complex, the P6(1)22 crystal structure was solved by molecular replacement with the CPMV model determined in the cubic cell.

Imaging RNA and dynamic protein segments with low-resolution virus crystallography: experimental design, data processing and implications of electron density maps

Single crystal diffraction data were collected from virus crystals in the resolution range of 270 to 14 A using a synchrotron X-ray source and a small-angle scattering instrument adapted for single crystal measurements. Reflections were measured from single crystals of the capsid of the double-stranded DNA bacteriophage HK97 and synthetic Flock House virus-like particles (sFHV). The quality of the low-resolution measurements was confirmed by excellent scaling statistics for both data sets. The sFHV amplitudes between 270 and 90 A resolution were closely similar to independently measured solution scattering data, and to data calculated from the Fourier transform of a uniform density sphere of 315 A diameter. A rotation function computed with the sFHV data between 70 and 20 A resolution was readily interpretable. A uniform density sphere model was used to compute phases for measured amplitudes between 270 and 68 A resolution. The calculated phases were refined and extended to 14 A resolution with real space averaging employing an external mask shape defined by the high-resolution structure. The resulting electron density map displayed regions interpretable as loosely ordered RNA that connected ordered RNA segments seen in a published 3.0 A resolution map. The published high-resolution electron density map lacked data inside 15 A resolution and the interior of the particle in that map appeared hollow. Difference electron density maps corresponding to bulk RNA were computed by subtracting the contribution of the protein shell, based on the available high-resolution atomic model, from either the cryo-electron microscopy density or the low-resolution X-ray density. Features of the RNA were closely similar in the cryo-electron microscopy and X-ray maps, demonstrating the consistency of the two imaging methods. Electron density maps computed at 14 and 6 A resolution with the X-ray amplitudes showed that RNA contributed little to the scattering beyond 14 A resolution.

Ab initio phase determination and phase extension using non-crystallographic symmetry

Non-crystallographic symmetry (NCS) can be used to improve, extend or find ab initio phases to be associated with a set of observed structure amplitudes, resulting in an interpretable electron-density map. The simplest application is merely to improve the accuracy of the phases by cyclically averaging the electron density, Fourier back-transformation of the modified map, and recomputing a new map with the newly found phases. The first sophistication of this procedure is to phase extend, in successive small steps, the currently available phase information to higher resolution, where only observed amplitudes were previously available. A further sophistication is to initiate the phase extension from very low resolution where a simple geometric model, or an electron microscope image, would be consistent with the chosen resolution. A number of recent examples of virus structure determination exist where such ab initio phasing was successful. The ultimate ab initio phase determination would be to extend phases given only an estimate of the F(000) term.

Nucleotide sequence of the bean strain of southern bean mosaic virus

The genome of the bean strain of southern bean mosaic virus (SBMV-B) comprises 4109 nucleotides and thus is slightly shorter than those of the two other sequenced sobemoviruses (southern bean mosaic virus, cowpea strain (SBMV-C) and rice yellow mottle virus (RYMV)). SBMV-B has an overall sequence similarity with SBMV-C of 55% and with RYMV of 45%. Three potential open reading frames (ORFs) were recognized in SBMV-B which were in similar positions in the genomes of SBMV-C and RYMV. However, there was no analog of SBMV-C and RYMV ORF 3. From a comparison of the predicted sequences of the ORFs of these three sobemoviruses and of the noncoding regions, it is suggested that the two SBMV strains differ from one another as much as they do from RYMV and that they should be considered as different viruses.

The atomic structure of Mengo virus at 3.0 A resolution

The structure of Mengo virus, a representative member of the cardio picornaviruses, is substantially different from the structures of rhino- and polioviruses. The structure of Mengo virus was solved with the use of human rhinovirus 14 as an 8 A resolution structural approximation. Phase information was then extended to 3 A resolution by use of the icosahedral symmetry. This procedure gives promise that many other virus structures also can be determined without the use of the isomorphous replacement technique. Although the organization of the major capsid proteins VP1, VP2, and VP3 of Mengo virus is essentially the same as in rhino- and polioviruses, large insertions and deletions, mostly in VP1, radically alter the surface features. In particular, the putative receptor binding "canyon" of human rhinovirus 14 becomes a deep "pit" in Mengo virus because of polypeptide insertions in VP1 that fill part of the canyon. The minor capsid peptide, VP4, is completely internal in Mengo virus, but its association with the other capsid proteins is substantially different from that in rhino- or poliovirus. However, its carboxyl terminus is located at a position similar to that in human rhinovirus 14 and poliovirus, suggesting the same autocatalytic cleavage of VP0 to VP4 and VP2 takes place during assembly in all these picornaviruses.

Effect of errors, redundancy, and solvent content in the molecular replacement procedure for the structure determination of biological macromolecules

The power of molecular replacement as a tool for analyzing macromolecular structures such as viruses has been demonstrated by an increasing number of successful determinations. We examine here the effects of noncrystallographic redundancy, N; the fraction of solvent volume (1- U/V); error in structure amplitude measurements, R; the fraction, f, of the unique data that were measured; error in the description of the noncrystallographic symmetry; and definition of the molecular envelope. The formula P = (Nf)1/2/R(U/V) has been derived and represents the inherent phasing power (P) for a given problem. The ability of "solvent flattening" procedures to determine phases was analyzed and found to be analogous to the effect of noncrystallographic redundancy. However, in the limiting case, the effect of solvent flattening approaches the power of Sayre's equations.

Structure of the Mengo virion. VII. Crystallization and preliminary X-ray diffraction analysis

Crystals of Mengo virions have been grown reproducibly and analyzed by X-ray diffraction. These crystals diffract to a resolution of 7.0 A. The unit cell exhibits cubic symmetry with a = 422 A. The space group is P23, with four virus particles situated on crystallographic threefold axes. Picornavirions from three of the four recognized genera (Study Group on Picornaviridae, Intervirology 10, 165-180, 1978) have now been examined at low resolution by X-ray diffraction: poliovirus type 1 (J. T. Finch and A. Klug, Nature (London) 183, 1709-1714, 1959; J. M. Hogle, J. Mol. Biol. 160, 663-668, 1982); human rhinovirus 14 (J. W. Erickson, E. A. Frankenberger, M. G. Rossmann, G. S. Fout, K. C. Medappa, and R. R. Rueckert, Proc. Natl. Acad. Sci. USA 80, 931-934, 1983); and Mengo virus.

A Description of the Techniques and Application of Molecular Replacement Used to Determine the Structure of Polyoma Virus Capsid at 22.5 Å Resolution

The electron density map of polyoma virus capsid crystals solved at 22.5 Å resolution by molecular replacement [Rayment, Baker, Caspar & Murakami (1982). Nature (London), 295, 110-115] shows that the 72 capsomeres that form the polyoma capsid are all pentamers. An extensive series of refinement calculations were undertaken to demonstrate the validity of this unexpected result. This report describes the details of the data collection, structure determination and the tests of the methods applied. The refinement calculations demonstrate that the refined phases are insensitive to the initial phasing model for a wide variety of models. They also show that it is vital to include in the refinement calculations interpolated values for the unrecorded data. A variety of tests demonstrate that the all-pentamer structure of the polyoma capsid is determined by the diffraction amplitudes and the self-consistent constraint that the 72 capsomeres are arranged with icosahedral symmetry within a well defined limiting envelope.

Polyoma virus capsid structure at 22.5 A resolution

X-ray diffraction data from polyoma capsid crystals were phased by refinement of low-resolution starting models to obtain a self-consistent structural solution. The unexpected result that the hexavalent morphological unit is a pentamer shows that specificity of bonding is not conserved among the protein subunits in the icosahedrally symmetric capsid.