The RNA of turnip yellow mosaic virus exhibits icosahedral order

Larson, Steven B.; Lucas, Robert W.; Greenwood, Aaron; McPherson, Alexander

doi:10.1016/j.virol.2005.01.036

Cited by 27 publications

(21 citation statements)

References 55 publications

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“…It is not known if nucleocapsid self-assembly is aided by cellular factors. Unlike some viruses (e.g., turnip yellow mosaic virus; Larson et al, 2005), VEEV nucleocapsid assembly does not appear to be directed by an icosahedral viral RNA scaffold, since viral RNA purified from mature VEEV had an extended structure (as observed by negative-stained electron microscope; data not shown).…”

Section: Discussionmentioning

confidence: 93%

Structure of a Venezuelan equine encephalitis virus assembly intermediate isolated from infected cells

et al. 2010

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Venezuelan equine encephalitis virus (VEEV) is a prototypical enveloped ssRNA virus of the family Togaviridae. To better understand alphavirus assembly, we analyzed newly formed nucleocapsid particles (termed pre-viral nucleocapsids) isolated from infected cells. These particles were intermediates along the virus assembly pathway, and ultimately bind membrane-associated viral glycoproteins to bud as mature infectious virus. Purified pre-viral nucleocapsids were spherical with a unimodal diameter distribution. The structure of one class of pre-viral nucleocapsids was determined with single particle reconstruction of cryo-electron microscopy images. These studies showed that pre-viral nucleocapsids assembled into an icosahedral structure with a capsid stoichiometry similar to the mature nucleocapsid. However, the individual capsomers were organized significantly differently within the pre-viral and mature nucleocapsids. The pre-viral nucleocapsid structure implies that nucleocapsids are highly plastic and undergo glycoprotein and/or lipid-driven rearrangements during virus self-assembly. This mechanism of self-assembly may be general for other enveloped viruses.

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Section: Discussionmentioning

confidence: 93%

Structure of a Venezuelan equine encephalitis virus assembly intermediate isolated from infected cells

et al. 2010

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“…Cryo-transmission electron microscopy ͑TEM͒ [21][22][23] and x-ray crystallography [24][25][26] reveal, at angstrom-level resolution, highly symmetrical supramolecular assemblages. The structural information corresponds mainly to the rigid protein shell, or capsid, which encapsulates the viral genome.…”

Section: Introductionmentioning

confidence: 99%

Electrostatics of capsid-induced viral RNA organization

Forrey

Muthukumar

2009

The Journal of Chemical Physics

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We have addressed the role of electrostatics in the formation of genome structure in the Pariacoto virus, where substantial experimental data are available. We have used Langevin dynamics simulation of a coarse-grained model, based on the published crystal structure of the rigid portion of the Pariacoto capsid and including flexible N-terminal protein arms, attached to the rigid capsid at the appropriate locations. The inclusion of charged residues in our model was dictated solely by the location of charges inherent in the Pariacoto sequence itself. Although the viral genome and other exogenous RNA sequences used in experimental studies can assume secondary structures, we have intentionally used uniformly charged flexible polyelectrolyte lacking predetermined secondary structures as the substitute for the viral genome, in order to see whether the same final assembled genome structure emerges without invoking secondary RNA structures. The intent of our study was to investigate the internal environment presented by the capsid proteins of Pariacoto virus, specifically whether the topological features and electrostatic potential at the inner capsid surface can induce complexation of generic negatively charged polyelectrolyte into structures similar to those observed experimentally with packaged RNA. We find that the charge decoration on the interior of the capsid templates the assembly of the flexible polyelectrolyte, allowing hybridizationlike folding of similarly charged strands, and eventually organizing dodecahedral assembly of the polymer. Our results from a generic flexible polyelectrolyte for the assembled structure and bimodal monomer distribution are remarkably matched to that of the viral RNA found experimentally. Results of our work can be interpreted primarily as a consequence of electrostatics, as consideration of base-pairing has been omitted. We propose that our work supports the growing body of evidence that electrostatic interactions play a crucial role in RNA viral assembly and structure.

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“…Some examples are STMV, [69,82] BMV [52], PMV, [46] and TYMV. [83] Crystals of smaller, T = 1, viruses such as STMV and SPMV have proven easier to flash-cool, and this follows from their smaller unit cell dimensions and the arguments presented above. T = 3 viruses have shown themselves to be more challenging, and viruses of even larger sizes and greater T numbers the most difficult of all.…”

Section: Crystal Considerationsmentioning

confidence: 99%

“…In a number of virus particles whose structures were solved by X-ray crystallography, fragments of nucleic acid, generally double helical, [182][183][184][185] but not always, [46,83,157,186] appeared in electron density maps. Figure 29 shows an example.…”

Section: Refinement Of Virus Crystal Structuresmentioning

confidence: 99%

“…By using such a structure factor difference Fourier synthesis, a substantial portion of the structured RNA in TYMV was visualized. [83] In cases where crystallographic symmetry is low, the symmetry of the icosahedral virus often is seen as pseudosymmetry in the diffraction pattern. Even in cases where it is not obvious to the eye, statistical searches such as the rotation function can detect it.…”

Section: Refinement Of Virus Crystal Structuresmentioning

confidence: 99%

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A guide to the crystallographic analysis of icosahedral viruses

McPherson

Larson

2015

Crystallography Reviews

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Determining the structure of an icosahedral virus crystal by X-ray diffraction follows very much the same course as conventional protein crystallography. The major differences arise from the relatively large sizes of the particles, which significantly affect the data collection process, data processing and management, and later, the refinement of a model. Most of the other differences are due to the high 5 3 2 point group symmetry of icosahedral viruses. This alters dramatically the means by which initial phases are obtained by molecular substitution, extended to higher resolution by electron density averaging and density modification, and the refinement of the structure in the light of high non-crystallographic symmetry. In this review, we attempt to lead the investigator through the various steps involved in solving the structure of a virus crystal. These steps include the purification of viruses, their crystallization, the recording of X-ray diffraction data, and its reduction to structure amplitudes. It further addresses the problems attending phase determination and ultimately the refinement of a model. Finally, we describe the unique properties of virus crystals and the factors that influence their physical and diffraction properties.

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The RNA of turnip yellow mosaic virus exhibits icosahedral order

Cited by 27 publications

References 55 publications

Structure of a Venezuelan equine encephalitis virus assembly intermediate isolated from infected cells

Structure of a Venezuelan equine encephalitis virus assembly intermediate isolated from infected cells

Electrostatics of capsid-induced viral RNA organization

A guide to the crystallographic analysis of icosahedral viruses

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