scholarly journals Structure of Double-Shelled Rice Dwarf Virus

1998 ◽  
Vol 72 (11) ◽  
pp. 8541-8549 ◽  
Author(s):  
Guangying Lu ◽  
Z. Hong Zhou ◽  
Matthew L. Baker ◽  
Joanita Jakana ◽  
Deyou Cai ◽  
...  
Keyword(s):  
Crop Production ◽  
Rna Virus ◽  
Mass Density ◽  
Three Dimensional ◽  
Outer Shell ◽  
Dwarf Virus ◽  
Dimensional Structure ◽  
Rice Dwarf Virus ◽  
Structural Match ◽  
Economic Threat

ABSTRACT Rice dwarf virus (RDV), a member of the Reoviridaefamily, is a double-stranded RNA virus. Infection of rice plants with RDV reduces crop production significantly and can pose a major economic threat to Southeast Asia. A 25-Å three-dimensional structure of the 700-Å-diameter RDV capsid has been determined by 400-kV electron cryomicroscopy and computer reconstruction. The structure revealed two distinctive icosahedral shells: a T=13l outer icosahedral shell composed of 260 trimeric clusters of P8 (46 kDa) and an inner T=1 icosahedral shell of 60 dimers of P3 (114 kDa). Sequence and structural comparisons were made between the RDV outer shell trimer and the two crystal conformations (REF and HEX) of the VP7 trimer of bluetongue virus, an animal analog of RDV. The low-resolution structural match of the RDV outer shell trimer to the HEX conformation of VP7 trimer has led to the proposal that P8 consists of an upper domain of β-sandwich motif and a lower domain of α helices. The less well fit REF conformation of VP7 to the RDV trimer may be due to the differences between VP7 and P8 in the sequence of the hinge region that connects the two domains. The additional mass density and the absence of a known signaling peptide on the surface of the RDV outer shell trimer may be responsible for the different interactions between plants and animal reoviruses.

The Three-dimensional structure of frozen-hydrated nudaurelia capensis β virus

1987 ◽  
Vol 45 ◽  
pp. 650-651
Author(s):  
N. H. Olson ◽  
T. S. Baker ◽  
Wu Bo Mu ◽  
J. E. Johnson ◽  
D. A. Hendry
Keyword(s):  
South African ◽  
Rna Virus ◽  
Carbon Film ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Electron Dose ◽  
Total Electron ◽  
Three Dimensional Structure ◽  
Negative Stain ◽  
Dimensional Reconstruction

Nudaurelia capensis β virus (NβV) is an RNA virus of the South African Pine Emperor moth, Nudaurelia cytherea capensis (Lepidoptera: Saturniidae). The NβV capsid is a T = 4 icosahedron that contains 60T = 240 subunits of the coat protein (Mr = 61,000). A three-dimensional reconstruction of the NβV capsid was previously computed from visions embedded in negative stain suspended over holes in a carbon film. We have re-examined the three-dimensional structure of NβV, using cryo-microscopy to examine the native, unstained structure of the virion and to provide a initial phasing model for high-resolution x-ray crystallographic studiesNβV was purified and prepared for cryo-microscopy as described. Micrographs were recorded ∼1 - 2 μm underfocus at a magnification of 49,000X with a total electron dose of about 1800 e-/nm2.

Three-Dimensional Structure of Rotavirus-Fab Complex

1990 ◽  
Vol 48 (1) ◽  
pp. 238-239
Author(s):  
B.V.V. Prasad ◽  
E. Marietta ◽  
J.W. Burns ◽  
M.K. Estes ◽  
W. Chiu
Keyword(s):  
Image Processing ◽  
Smooth Surface ◽  
Three Dimensional ◽  
Outer Shell ◽  
Dimensional Structure ◽  
Structural Studies ◽  
Cell Penetration ◽  
Electron Cryomicroscopy ◽  
Image Processing Techniques ◽  
Processing Techniques

Rotaviruses are spherical, double-shelled particles. They have been identified as a major cause of infantile gastroenteritis worldwide. In our earlier studies we determined the three-dimensional structures of double-and single-shelled simian rotavirus embedded in vitreous ice using electron cryomicroscopy and image processing techniques to a resolution of 40Å. A distinctive feature of the rotavirus structure is the presence of 132 large channels spanning across both the shells at all 5- and 6-coordinated positions of a T=13ℓ icosahedral lattice. The outer shell has 60 spikes emanating from its relatively smooth surface. The inner shell, in contrast, exhibits a bristly surface made of 260 morphological units at all local and strict 3-fold axes (Fig.l).The outer shell of rotavirus is made up of two proteins, VP4 and VP7. VP7, a glycoprotein and a neutralization antigen, is the major component. VP4 has been implicated in several important functions such as cell penetration, hemagglutination, neutralization and virulence. From our earlier studies we had proposed that the spikes correspond to VP4 and the rest of the surface is composed of VP7. Our recent structural studies, using the same techniques, with monoclonal antibodies specific to VP4 have established that surface spikes are made up of VP4.

scholarly journals Structure of Isolated Nucleocapsids from Venezuelan Equine Encephalitis Virus and Implications for Assembly and Disassembly of Enveloped Virus

2003 ◽  
Vol 77 (1) ◽  
pp. 659-664 ◽  
Author(s):  
Angel Paredes ◽  
Kathy Alwell-Warda ◽  
Scott C. Weaver ◽  
Wah Chiu ◽  
Stanley J. Watowich
Keyword(s):  
Conformational Changes ◽  
Rna Virus ◽  
Three Dimensional ◽  
Venezuelan Equine Encephalitis Virus ◽  
Encephalitis Virus ◽  
Dimensional Structure ◽  
Icosahedral Symmetry ◽  
Venezuelan Equine Encephalitis ◽  
Equine Encephalitis Virus ◽  
Enveloped Virus

ABSTRACT Venezuelan equine encephalitis virus (VEEV) is an important human and equine pathogen in the Americas, with widespread reoccurring epidemics extending from South America to the southern United States. Most troubling, VEEV has been made into a weapon by several countries and is currently restricted by the Centers for Disease Control and Prevention as a potential biological warfare and terrorism agent. To facilitate the development of antiviral compounds, the structure of the nucleocapsid isolated from VEEV has been determined by electron cryomicroscopy and image reconstruction and represents the first three-dimensional structure of a nucleocapsid isolated from a single-stranded enveloped RNA virus. The isolated VEEV nucleocapsid undergoes significant reorganization relative to its structure within VEEV. However, the isolated nucleocapsid clearly exhibits T=4 icosahedral symmetry, and its characteristic nucleocapsid hexons and pentons are preserved. The diameter of the isolated nucleocapsid is ∼11.5% larger than that of the nucleocapsid within VEEV, with radial expansion being greatest near the hexons. Significantly, this is the first direct structural evidence showing that a simple enveloped virus undergoes large conformational changes during maturation, suggesting that the lipid bilayer and the transmembrane proteins of simple enveloped viruses provide the energy necessary to reorganize the nucleocapsid during maturation.

scholarly journals Mutations in the palm region of a plus-strand RNA virus polymerase result in attenuated phenotype

2006 ◽  
Vol 87 (12) ◽  
pp. 3631-3636 ◽  
Author(s):  
Andreas Gallei ◽  
Simone Widauer ◽  
Heinz-Jürgen Thiel ◽  
Paul Becher
Keyword(s):  
Viral Vectors ◽  
Rna Virus ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Diarrhea Virus ◽  
Interesting Insight ◽  
Plaque Phenotype ◽  
Viral Attenuation ◽  
Viral Diarrhea Virus

The three-dimensional structure of RNA-dependent RNA polymerases (RdRps) is highly conserved among RNA viruses. In a previous study, a unique set of mutant strains of Bovine viral diarrhea virus was obtained, encompassing either a genomic deletion of six codons or duplications of between 1 and 45 codons; these mutations affect different parts of the palm region, the most conserved part of RdRps containing the catalytic centre. In the present study, a detailed characterization of the RdRp mutant viruses was performed, demonstrating different degrees of a small-plaque phenotype in cell culture, correlating with significantly reduced viral RNA synthesis and delayed virus replication. Taken together, the results of this study demonstrate a surprising flexibility within the palm region of a plus-strand RNA virus RdRp, resulting in viral attenuation in vitro. This interesting insight into an essential viral protein may have implications for the development of vaccines and attenuated viral vectors.

scholarly journals A Novel Iflavirus Was Discovered in Green Rice Leafhopper Nephotettix cincticeps and Its Proliferation Was Inhibited by Infection of Rice Dwarf Virus

2021 ◽  
Vol 11 ◽  
Author(s):  
Wenxi Jia ◽  
Fei Wang ◽  
Jingjing Li ◽  
Xuefei Chang ◽  
Yi Yang ◽  
...  
Keyword(s):  
Infection Rate ◽  
Rna Virus ◽  
Antagonistic Effect ◽  
Dwarf Virus ◽  
Insect Vector ◽  
Rice Dwarf Virus ◽  
Reading Frame ◽  
Green Rice Leafhopper ◽  
Laboratory Populations ◽  
Dwarf Disease

The green rice leafhopper, Nephotettix cincticeps (Hemiptera: Cicadellidae), is a key insect vector transmitting rice dwarf virus (RDV) that causes rice dwarf disease. We discovered a novel iflavirus from the transcriptomes of N. cincticeps and named it as Nephotettix cincticeps positive-stranded RNA virus-1 (NcPSRV-1). The viral genome consists of 10,524 nucleotides excluding the poly(A) tail and contains one predicted open reading frame encoding a polyprotein of 3,192 amino acids, flanked by 5' and 3' untranslated regions. NcPSRV-1 has a typical iflavirus genome arrangement and is clustered with the members of the family Iflaviridae in the phylogenetic analysis. NcPSRV-1 was detected in all tested tissues and life stages of N. cincticeps and could be transmitted horizontally and vertically. Moreover, NcPSRV-1 had high prevalence in the laboratory populations and was widely spread in field populations of N. cincticeps. NcPSRV-1 could also infect the two-striped leafhopper, Nephotettix apicalis, at a 3.33% infection rate, but was absent in the zigzag leafhopper, Recilia dorsalis, and rice Oryza sativa variety TN1. The infection of RDV altered the viral load and infection rate of NcPSRV-1 in N. cincticeps, for which it seems that RDV has an antagonistic effect on NcPSRV-1 infection in the host.

Electron microscopy of T4 DNA helix destabilizing protein (GP32*I) crystal

1983 ◽  
Vol 41 ◽  
pp. 728-729
Author(s):  
H.A. Cohen ◽  
W. Chiu ◽  
J. Hosoda
Keyword(s):  
Mass Density ◽  
Three Dimensional ◽  
Average Density ◽  
Dimensional Structure ◽  
Long Range Order ◽  
Alpha Helices ◽  
Negative Stain ◽  
T4 Phage ◽  
Density Map ◽  
Dna Helix

The DNA helix destabilizing protein of T4 phage, gp32, may be enzymatically cleaved to produce the major fragment gp32*I, which crystallizes as thin platelets suitable for electron diffraction and imaging. The low resolution three-dimensional structure of gp32*I was previously determined. That model, based on the exclusion of negative stain showed that the protein crystallizes as dimers about 90 Å high, with each monomer about 20 Å in diameter. Since negative stain limits possible resolution to about 15 Å, glucose embedding was used to maintain the long range order of the crystal. A projected mass density map was reconstructed to 7.6 Å which resolved five masses in each dimer. The map was difficult to interpret since the average density of the protein was only slightly less than that of the embedding media. As a consequence, regions of protein that are denser than average (e.g. alpha helices running perpendicular to the surface of the crystal) approach the mass density of the embedding glucose and thus are invisible.

Three-dimensional Structure of Penicillium chrysogenum virus: A Double-stranded RNA Virus with a Genuine T=1 Capsid

2003 ◽  
Vol 331 (2) ◽  
pp. 417-431 ◽  
Author(s):  
José R. Castón ◽  
Said A. Ghabrial ◽  
Daohong Jiang ◽  
Germán Rivas ◽  
Carlos Alfonso ◽  
...  
Keyword(s):  
Penicillium Chrysogenum ◽  
Rna Virus ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Double Stranded Rna ◽  
Three Dimensional Structure

scholarly journals Cryo-electron tomography of porcine reproductive and respiratory syndrome virus: organization of the nucleocapsid

2009 ◽  
Vol 90 (3) ◽  
pp. 527-535 ◽  
Author(s):  
Michael S. Spilman ◽  
Craig Welbon ◽  
Eric Nelson ◽  
Terje Dokland
Keyword(s):  
Gap Analysis ◽  
Electron Tomography ◽  
Protein Complexes ◽  
Rna Virus ◽  
Tomographic Reconstruction ◽  
Three Dimensional ◽  
Average Diameter ◽  
Dimensional Structure ◽  
Respiratory Syndrome Virus ◽  
Nucleocapsid Proteins

Porcine reproductive and respiratory virus (PRRSV) is an enveloped positive-sense RNA virus of the family Arteriviridae that causes severe and persistent disease in pigs worldwide. The PRRSV virion consists of a lipid envelope that contains several envelope proteins surrounding a nucleocapsid core that encapsidates the RNA genome. To provide a better understanding of the structure and assembly of PRRSV, we have carried out cryo-electron microscopy and tomographic reconstruction of virions grown in MARC-145 cells. The virions are pleomorphic, round to egg-shaped particles with an average diameter of 58 nm. The particles display a smooth outer surface with only a few protruding features, presumably corresponding to the envelope protein complexes. The virions contain a double-layered, hollow core with an average diameter of 39 nm, which is separated from the envelope by a 2–3 nm gap. Analysis of the three-dimensional structure suggests that the core is composed of a double-layered chain of nucleocapsid proteins bundled into a hollow ball.

scholarly journals Quantitative and dynamic measurements of biological fresh samples with X-ray phase contrast tomography

2014 ◽  
Vol 21 (6) ◽  
pp. 1347-1357 ◽  
Author(s):  
Masato Hoshino ◽  
Kentaro Uesugi ◽  
Takuro Tsukube ◽  
Naoto Yagi
Keyword(s):  
Phase Contrast ◽  
Morphological Changes ◽  
Mass Density ◽  
Three Dimensional ◽  
Measurement Procedure ◽  
Dimensional Structure ◽  
Fresh Sample ◽  
Mouse Fetus ◽  
X Ray ◽  
Phase Contrast Tomography

X-ray phase contrast tomography using a Talbot grating interferometer was applied to biological fresh samples which were not fixed by any fixatives. To achieve a high-throughput measurement for the fresh samples the X-ray phase contrast tomography measurement procedure was improved. The three-dimensional structure of a fresh mouse fetus was clearly depicted as a mass density map using X-ray phase contrast tomography. The mouse fetus measured in the fresh state was then fixed by formalin and measured in the fixed state. The influence of the formalin fixation on soft tissue was quantitatively evaluated by comparing the fresh and fixed samples. X-ray phase contrast tomography was also applied to the dynamic measurement of a biological fresh sample. Morphological changes of a ring-shaped fresh pig aorta were measured tomographically under different degrees of stretching.

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