Atomic model of an infectious rotavirus particle

Settembre, Ethan C.; Chen, James Z.; Dormitzer, Philip R.; Grigorieff, Nikolaus; Harrison, Stephen C.

doi:10.1038/emboj.2010.322

Cited by 266 publications

(365 citation statements)

References 39 publications

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“…Clearly resolved densities are observed not merely for bulky side chains such as tryptophan and tyrosine, but also for extended side chains such as arginine and lysine and smaller side chains such as Leu, Ile, and Val (Figs. [3][4][5]. Interestingly, densities for positively charged and neutral residues are clearly resolved in virtually all instances (see selected Arg, Lys, His, and Gln residues shown in Fig.…”

Section: Significancementioning

confidence: 99%

“…single-particle EM | frame alignment | CTF determination | 3D reconstruction | structure refinement R apid advances in technology for single-particle cryo-electron microscopy (cryo-EM) over the last few years have made it possible to determine high-resolution structures of large and well-ordered macromolecular assemblies such as 2D protein crystals, helical lattices, icosahedral viruses, and protein complexes with high symmetry (1)(2)(3)(4)(5)(6)(7)(8)(9)(10). More recently, continuing developments in microscope hardware and image processing software have yielded near-atomic resolution information for two smallersized complexes with low symmetry, the 700-kDa proteasome (11) and a 300-kDa mammalian ion channel (12), and for larger assemblies with no symmetry such as ribosome complexes (13)(14)(15).…”

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confidence: 99%

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Structure of β-galactosidase at 3.2-Å resolution obtained by cryo-electron microscopy

Bartesaghi

Matthies

Banerjee

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

202

178

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We report the solution structure of Escherichia coli β-galactosidase (∼465 kDa), solved at ∼3.2-Å resolution by using single-particle cryo-electron microscopy (cryo-EM). Densities for most side chains, including those of residues in the active site, and a catalytic Mg 2+ ion can be discerned in the map obtained by cryo-EM. The atomic model derived from our cryo-EM analysis closely matches the 1.7-Å crystal structure with a global rmsd of ∼0.66 Å. There are significant local differences throughout the protein, with clear evidence for conformational changes resulting from contact zones in the crystal lattice. Inspection of the map reveals that although densities for residues with positively charged and neutral side chains are well resolved, systematically weaker densities are observed for residues with negatively charged side chains. We show that the weaker densities for negatively charged residues arise from their greater sensitivity to radiation damage from electron irradiation as determined by comparison of density maps obtained by using electron doses ranging from 10 to 30 e − /Å 2 . In summary, we establish that it is feasible to use cryo-EM to determine near-atomic resolution structures of protein complexes (<500 kDa) with low symmetry, and that the residue-specific radiation damage that occurs with increasing electron dose can be monitored by using dose fractionation tools available with direct electron detector technology.single-particle EM | frame alignment | CTF determination | 3D reconstruction | structure refinement R apid advances in technology for single-particle cryo-electron microscopy (cryo-EM) over the last few years have made it possible to determine high-resolution structures of large and well-ordered macromolecular assemblies such as 2D protein crystals, helical lattices, icosahedral viruses, and protein complexes with high symmetry (1-10). More recently, continuing developments in microscope hardware and image processing software have yielded near-atomic resolution information for two smallersized complexes with low symmetry, the 700-kDa proteasome (11) and a 300-kDa mammalian ion channel (12), and for larger assemblies with no symmetry such as ribosome complexes (13-15). These developments signal an important change in the way cryo-EM can now be used in structural biology. Rather than simply using cryo-EM maps, typically in the 6-to 20-Å resolution range, as an envelope in which to fit structures obtained by X-ray crystallography, there is the exciting prospect of using cryo-EM to derive de novo, high-resolution structural models of proteins in one or multiple functional conformational states.The preparation of specimens for cryo-EM involves rapid plunge freezing of a thin aqueous suspension into liquid ethane cooled by liquid nitrogen. The speed of freezing is estimated to be ∼10 7 K/s (16), enabling the rapid cooling of the aqueous medium into a glass-like state. This rapid cooling traps the macromolecular components in a near-native state, capturing the conformational distribution and spa...

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Section: Significancementioning

confidence: 99%

mentioning

confidence: 99%

Structure of β-galactosidase at 3.2-Å resolution obtained by cryo-electron microscopy

Bartesaghi

Matthies

Banerjee

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

202

178

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“…The middle layer is formed by up to 260 VP6 trimers that interact with VP2 dimers to stabilize the core shell (Mathieu et al 2001). The outer layer is composed of VP7 and VP4: VP7 constitutes a large part of the outer layer and makes extensive contact with the middle layer, whereas VP4 protrudes radially from the particle as spike-like structures (Settembre et al 2011). A viral intermediate containing the core shell and middle layer is called a doublelayer particle (DLP) and a mature infectious particle harboring all three layers is referred to as a triple-layer particle (TLP).…”

Section: Viruses Co-opt the Er For Infectionmentioning

confidence: 99%

How Viruses Use the Endoplasmic Reticulum for Entry, Replication, and Assembly

Inoue

Tsai

2013

Cold Spring Harbor Perspectives in Biology

105

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“…The external layer of the virus is discontinuous and looks like a sponge, because of the multiple small extensions of the VP4 spike (Settembre et al, 2011). The structural proteins of the virion are depicted as three concentric circles, forming an equal number of layers around the dsRNA genome (triple layered particle) (McClain et al, 2010).…”

Section: Structure and Classification Of The Virusmentioning

confidence: 99%

Rotavirus infections in domestic animals

Chatzopoulos

Athanasiou

Spyrou

et al. 2017

J Hellenic Vet Med Soc

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ABSTRACT. Rotaviruses are major enteric pathogens of humans and a wide variety of animals. Rotavirus infections have a worldwide prevalence. The viral genome is composed of 11 double-stranded RNA segments with six structural and five or six non-structural proteins. Over 35,000 strains have been identified and classified into five main (A, B, C, D, E) and three additional tentative (F, G, H) serotype groups. A binary classification system has been proposed defining 'G' or 'P' types, with at least 27 G and 35 P genotypes reported thusfar. The virus is transmitted primarily by the faecal-oral and oral routes. After attachment, entry into the host cells occurs through direct entry, fusion or endocytosis. Main mechanisms of Rotavirus-induced diarrhoea involve extensive enterocyte losses and nutrient disdigestion and malabsorption. Clinical features of Rotavirus infections range from asymptomatic infections to fulminant disease leading to rapid death. In calves, lambs and kids, piglets and foals, salient sign of the disease is diarrhoea; diarrhoeic faeces are white, yellow or, in severe cases, blood-tinted or frank haemorrhagic. In dogs and cats, the infection occurs usually as self-limiting diarrhoea. Avian Rotavirus infections are characterized by enteritis, growth depression and/or growth retardation. Definitive diagnosis of the infection can only be achieved by laboratory tests, including electron microscopic examination, immunohistochemical examination, immunofluorescence, ELISA, latex agglutination and molecular techniques. There is no specific treatment against Rotavirus infections. Treatment is based in providing supportive care and managing clinical signs and potential complications. Effective vaccines, containing inactivated, recombinant or attenuated strains of the virus, are available. Challenge studies have shown the ease of the virus in cross-infecting various animal species; animal strains of the virus may cross species and infect humans. Due to the ability of the virus to overcome species barriers, animal strains may act as natural source of viral genomes, promoting mutations and creating new viral genotypes, whose virulence cannot be predictable.

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Atomic model of an infectious rotavirus particle

Cited by 266 publications

References 39 publications

Structure of β-galactosidase at 3.2-Å resolution obtained by cryo-electron microscopy

Structure of β-galactosidase at 3.2-Å resolution obtained by cryo-electron microscopy

How Viruses Use the Endoplasmic Reticulum for Entry, Replication, and Assembly

Rotavirus infections in domestic animals

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