Three-dimensional Structure of Satellite Tobacco Mosaic Virus at 2·9 Å Resolution

Sb, Larson; Koszelak, Stanley; Day, John; Greenwood, Aaron; Dodds, J. A.; McPherson, Alexander

doi:10.1006/jmbi.1993.1289

Cited by 58 publications

(41 citation statements)

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“…X-ray diffraction analysis of crystals of STMV [7][8][9] reveals icosahedrally disposed doublehelical segments of RNA, each composed of nine base pairs plus stacked bases at either 3′ terminus. In addition, a single, well-defined but isolated nucleotide with about half occupancy is bound by the coat proteins.…”

Section: Figurementioning

confidence: 99%

“…Protein-RNA interactions initiate as capsid protein dimers bind to RNA stem-loop elements. Finally, capsid protein dimers, associated with RNA stem-loops, cooperatively interact with one another and with disparate RNA elements [7,8] to form the virion.…”

Section: A Model For Assemblymentioning

confidence: 99%

“…Secondary structure prediction [2,3] indicates possible base pairing approaching 70%, a feature shared by other satellite viruses and satellite RNAs [4][5][6]. Its 1.8 Å X-ray structure [7][8][9] revealed double-helical segments of RNA centered on all dyad axes of the virion, 30 in all, In addition, an isolated nucleotide having an occupancy of half that of the helical nucleotides was observed some distance from the ends of each helix, apparently an ordered component of an otherwise disordered region of the RNA. The helical segments of encapsidated RNA, which reflect the icosahedrally averaged structure, comprise nine base pairs, plus additional nucleotides stacked on the helix ends.…”

Section: Introductionmentioning

confidence: 99%

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Satellite tobacco mosaic virus RNA: structure and implications for assembly

Larson

McPherson

2001

Current Opinion in Structural Biology

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Section: Figurementioning

confidence: 99%

Section: A Model For Assemblymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Satellite tobacco mosaic virus RNA: structure and implications for assembly

Larson

McPherson

2001

Current Opinion in Structural Biology

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“…The image reconstruction of microscopy data showed that RNA folding in the dodecahedral RNA cage occurred independent of the specific sequence of RNA. In addition, we note that in cases where x-ray diffraction and cryo-TEM have demonstrated symmetrical ordering in ss-RNA viruses, the ordered parts of the viral genome are associated with specific regions along the inner capsid surface [32][33][34][35][36] perhaps containing an excess of fixed positive charges. Combining these experimental facts and our previous theoretical work demonstrating the dominance of electrostatic forces in RNA virus assembly, we conjecture that the Pariacoto capsid itself provides a nonsequence-specific opportunity for the templated assembly of negatively charged RNA and that the observed dodecahedral structure of the RNA is "preprogrammed" by the capsid independently of the details of the secondary structure of the RNA from which it is formed.…”

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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“…[1][2][3][4] This is indicated as well by analyses of viral RNAs in terms of probable secondary structure arrangements. 5,6 X-ray crystallographic analyses of some viruses from both plants and insects have demonstrated the presence of helical RNA within capsids.…”

Section: Introductionmentioning

confidence: 99%

Atomic Force Microscopy Analysis of Icosahedral Virus RNA

Kuznetsov

Daijogo

Zhou

et al. 2005

Journal of Molecular Biology

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Single-stranded genomic RNAs from four icosahedral viruses (poliovirus, turnip yellow mosaic virus (TYMV), brome mosaic virus (BMV), and satellite tobacco mosaic virus (STMV)) along with the RNA from the helical tobacco mosaic virus (TMV) were extracted using phenol/chloroform. The RNAs were imaged using atomic force microscopy (AFM) under dynamic conditions in which the RNA was observed to unfold. RNAs from the four icosahedral viruses initially exhibited highly condensed, uniform spherical shapes with diameters consistent with those expected from the interiors of their respective capsids. Upon incubation at 26 8C, poliovirus RNA gradually transformed into chains of globular domains having the appearance of thick, irregularly segmented fibers. These ultimately unwound further to reveal segmented portions of the fibers connected by single strands of RNA of 0.5-1 nm thickness. Virtually the same transformations were shown by TYMV and BMV RNA, and with heating, the RNA from STMV. Upon cooling, the chains of domains of poliovirus RNA and STMV RNA condensed and re-formed their original spherical shapes. TMV RNAs initially appeared as single-stranded threads of 0.5-1.0 nm diameter but took on the structure of the multidomain chains upon further incubation at room temperature. These ultimately condensed into short, thick chains of larger domains. Our observations suggest that classical extraction of RNA from icosahedral virions produces little effect on overall conformation. As tertiary structure is lost however, it is evident that secondary structural elements are arranged in a sequential, linear fashion along the polynucleotide chain. At least in the case of poliovirus and STMV, the process of tertiary structure re-formation from the linear chain of secondary structural domains proceeds in the absence of protein. RNA base sequence, therefore, may be sufficient to encode the conformation of the encapsidated RNA even in the absence of coat proteins.

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Three-dimensional Structure of Satellite Tobacco Mosaic Virus at 2·9 Å Resolution

Cited by 58 publications

References 0 publications

Satellite tobacco mosaic virus RNA: structure and implications for assembly

Satellite tobacco mosaic virus RNA: structure and implications for assembly

Electrostatics of capsid-induced viral RNA organization

Atomic Force Microscopy Analysis of Icosahedral Virus RNA

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