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Viruses
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Advances in Structural Virology via Cryo-EM
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Advances in Structural Virology via Cryo-EM

A special issue of Viruses (ISSN 1999-4915).

Deadline for manuscript submissions: closed (15 February 2018) | Viewed by 53567

Special Issue Editor

Prof. Dr. Elizabeth R. Wright

E-Mail Website
Guest Editor
Department of Pediatrics, Emory University, Atlanta, GA, USA
Interests: Cryo-electron microscopy; cryo-electron tomography; correlative imaging; virus structure and assembly; enveloped viruses; bacteriophage; host-pathogen interactions

Special Issue Information

Dear Colleagues,

Recent advances in the technologies associated with cryo-electron microscopy (cryo-EM) have brought forward a 'resolution revolution'. This revolution has been harnessed by the structural virology community and has yielded significant results that have impacted our fundamental understanding of virus structure, virus glycoprotein structure, processes of virus replication, and anti-viral and vaccine development.

This Special Issue of Viruses is dedicated to advances in cryo-EM based structural virology. We would like to assemble a collection of primary research papers and reviews that will highlight developments in the field of structural virology made possible by advances in cryo-EM instrumentation and methods. Topics may include all areas of structural virology, as well as novel cryo-EM strategies, used to determine the structures of viruses and virus–host interactions.

Prof. Elizabeth R. Wright
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Cryo-electron microscopy (cryo-EM)

  • Cryo-electron tomography (cryo-ET)

  • Cryo-correlative light and electron microscopy (cryo-CLEM)

  • Virus fusion and entry

  • Virus assembly

  • Virus maturation

  • Vaccine, prophylactic antibody, and anti-viral development

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Published Papers (6 papers)

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Research

Jump to: Review

22 pages, 12635 KiB  
Article
The Morphology and Assembly of Respiratory Syncytial Virus Revealed by Cryo-Electron Tomography
by Zunlong Ke, Rebecca S. Dillard, Tatiana Chirkova, Fredrick Leon, Christopher C. Stobart, Cheri M. Hampton, Joshua D. Strauss, Devi Rajan, Christina A. Rostad, Jeannette V. Taylor, Hong Yi, Raven Shah, Mengtian Jin, Tina V. Hartert, R. Stokes Peebles, Jr., Barney S. Graham, Martin L. Moore, Larry J. Anderson and Elizabeth R. Wright
Viruses 2018, 10(8), 446; https://doi.org/10.3390/v10080446 - 20 Aug 2018
Cited by 57 | Viewed by 11500
Abstract
Human respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract disease in young children. With repeat infections throughout life, it can also cause substantial disease in the elderly and in adults with compromised cardiac, pulmonary and immune systems. RSV is [...] Read more.
Human respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract disease in young children. With repeat infections throughout life, it can also cause substantial disease in the elderly and in adults with compromised cardiac, pulmonary and immune systems. RSV is a pleomorphic enveloped RNA virus in the Pneumoviridae family. Recently, the three-dimensional (3D) structure of purified RSV particles has been elucidated, revealing three distinct morphological categories: spherical, asymmetric, and filamentous. However, the native 3D structure of RSV particles associated with or released from infected cells has yet to be investigated. In this study, we have established an optimized system for studying RSV structure by imaging RSV-infected cells on transmission electron microscopy (TEM) grids by cryo-electron tomography (cryo-ET). Our results demonstrate that RSV is filamentous across several virus strains and cell lines by cryo-ET, cryo-immuno EM, and thin section TEM techniques. The viral filament length varies from 0.5 to 12 μm and the average filament diameter is approximately 130 nm. Taking advantage of the whole cell tomography technique, we have resolved various stages of RSV assembly. Collectively, our results can facilitate the understanding of viral morphogenesis in RSV and other pleomorphic enveloped viruses. Full article
(This article belongs to the Special Issue Advances in Structural Virology via Cryo-EM)
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18 pages, 17196 KiB  
Article
Atomic Resolution Structures of Human Bufaviruses Determined by Cryo-Electron Microscopy
by Maria Ilyas, Mario Mietzsch, Shweta Kailasan, Elina Väisänen, Mengxiao Luo, Paul Chipman, J. Kennon Smith, Justin Kurian, Duncan Sousa, Robert McKenna, Maria Söderlund-Venermo and Mavis Agbandje-McKenna
Viruses 2018, 10(1), 22; https://doi.org/10.3390/v10010022 - 4 Jan 2018
Cited by 18 | Viewed by 10418
Abstract
Bufavirus strain 1 (BuV1), a member of the Protoparvovirus genus of the Parvoviridae, was first isolated from fecal samples of children with acute diarrhea in Burkina Faso. Since this initial discovery, BuVs have been isolated in several countries, including Finland, the Netherlands, [...] Read more.
Bufavirus strain 1 (BuV1), a member of the Protoparvovirus genus of the Parvoviridae, was first isolated from fecal samples of children with acute diarrhea in Burkina Faso. Since this initial discovery, BuVs have been isolated in several countries, including Finland, the Netherlands, and Bhutan, in pediatric patients exhibiting similar symptoms. Towards their characterization, the structures of virus-like particles of BuV1, BuV2, and BuV3, the current known genotypes, have been determined by cryo-electron microscopy and image reconstruction to 2.84, 3.79, and 3.25 Å, respectively. The BuVs, 65–73% identical in amino acid sequence, conserve the major viral protein, VP2, structure and general capsid surface features of parvoviruses. These include a core β-barrel (βB-βI), α-helix A, and large surface loops inserted between these elements in VP2. The capsid contains depressions at the icosahedral 2-fold and around the 5-fold axes, and has three separated protrusions surrounding the 3-fold axes. Structure comparison among the BuVs and to available parvovirus structures revealed capsid surface variations and capsid 3-fold protrusions that depart from the single pinwheel arrangement of the animal protoparvoviruses. These structures provide a platform to begin the molecular characterization of these potentially pathogenic viruses. Full article
(This article belongs to the Special Issue Advances in Structural Virology via Cryo-EM)
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11513 KiB  
Article
Cleavage and Structural Transitions during Maturation of Staphylococcus aureus Bacteriophage 80α and SaPI1 Capsids
by James L. Kizziah, Keith A. Manning, Altaira D. Dearborn, Erin A. Wall, Laura Klenow, Rosanne L. L. Hill, Michael S. Spilman, Scott M. Stagg, Gail E. Christie and Terje Dokland
Viruses 2017, 9(12), 384; https://doi.org/10.3390/v9120384 - 16 Dec 2017
Cited by 11 | Viewed by 5482
Abstract
In the tailed bacteriophages, DNA is packaged into spherical procapsids, leading to expansion into angular, thin-walled mature capsids. In many cases, this maturation is accompanied by cleavage of the major capsid protein (CP) and other capsid-associated proteins, including the scaffolding protein (SP) that [...] Read more.
In the tailed bacteriophages, DNA is packaged into spherical procapsids, leading to expansion into angular, thin-walled mature capsids. In many cases, this maturation is accompanied by cleavage of the major capsid protein (CP) and other capsid-associated proteins, including the scaffolding protein (SP) that serves as a chaperone for the assembly process. Staphylococcus aureus bacteriophage 80α is capable of high frequency mobilization of mobile genetic elements called S. aureus pathogenicity islands (SaPIs), such as SaPI1. SaPI1 redirects the assembly pathway of 80α to form capsids that are smaller than those normally made by the phage alone. Both CP and SP of 80α are N-terminally processed by a host-encoded protease, Prp. We have analyzed phage mutants that express pre-cleaved or uncleavable versions of CP or SP, and show that the N-terminal sequence in SP is absolutely required for assembly, but does not need to be cleaved in order to produce viable capsids. Mutants with pre-cleaved or uncleavable CP display normal viability. We have used cryo-EM to solve the structures of mature capsids from an 80α mutant expressing uncleavable CP, and from wildtype SaPI1. Comparisons with structures of 80α and SaPI1 procapsids show that capsid maturation involves major conformational changes in CP, consistent with a release of the CP N-arm by SP. The hexamers reorganize during maturation to accommodate the different environments in the 80α and SaPI1 capsids. Full article
(This article belongs to the Special Issue Advances in Structural Virology via Cryo-EM)
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7631 KiB  
Article
High-Resolution Structure Analysis of Antibody V5 and U4 Conformational Epitopes on Human Papillomavirus 16
by Jian Guan, Stephanie M. Bywaters, Sarah A. Brendle, Robert E. Ashley, Alexander M. Makhov, James F. Conway, Neil D. Christensen and Susan Hafenstein
Viruses 2017, 9(12), 374; https://doi.org/10.3390/v9120374 - 6 Dec 2017
Cited by 10 | Viewed by 8019
Abstract
Cancers attributable to human papillomavirus (HPV) place a huge burden on the health of both men and women. The current commercial vaccines are genotype specific and provide little therapeutic benefit to patients with existing HPV infections. Identifying the conformational epitopes on the virus [...] Read more.
Cancers attributable to human papillomavirus (HPV) place a huge burden on the health of both men and women. The current commercial vaccines are genotype specific and provide little therapeutic benefit to patients with existing HPV infections. Identifying the conformational epitopes on the virus capsid supports the development of improved recombinant vaccines to maximize long-term protection against multiple types of HPV. Fragments of antibody (Fab) digested from the neutralizing monoclonal antibodies H16.V5 (V5) and H16.U4 (U4) were bound to HPV16 capsids and the structures of the two virus-Fab complexes were solved to near atomic resolution using cryo-electron microscopy. The structures reveal virus conformational changes, the Fab-binding mode to the capsid, the residues comprising the epitope and indicate a potential interaction of U4 with the minor structural protein, L2. Competition enzyme-linked immunosorbent assay (ELISA) showed V5 outcompetes U4 when added sequentially, demonstrating a steric interference even though the footprints do not overlap. Combined with our previously reported immunological and structural results, we propose that the virus may initiate host entry through an interaction between the icosahedral five-fold vertex of the capsid and receptors on the host cell. The highly detailed epitopes identified for the two antibodies provide a framework for continuing biochemical, genetic and biophysical studies. Full article
(This article belongs to the Special Issue Advances in Structural Virology via Cryo-EM)
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Review

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22 pages, 3119 KiB  
Review
Breaking Symmetry in Viral Icosahedral Capsids as Seen through the Lenses of X-ray Crystallography and Cryo-Electron Microscopy
by Kristin N. Parent, Jason R. Schrad and Gino Cingolani
Viruses 2018, 10(2), 67; https://doi.org/10.3390/v10020067 - 7 Feb 2018
Cited by 28 | Viewed by 9711
Abstract
The majority of viruses on Earth form capsids built by multiple copies of one or more types of a coat protein arranged with 532 symmetry, generating an icosahedral shell. This highly repetitive structure is ideal to closely pack identical protein subunits and to [...] Read more.
The majority of viruses on Earth form capsids built by multiple copies of one or more types of a coat protein arranged with 532 symmetry, generating an icosahedral shell. This highly repetitive structure is ideal to closely pack identical protein subunits and to enclose the nucleic acid genomes. However, the icosahedral capsid is not merely a passive cage but undergoes dynamic events to promote packaging, maturation and the transfer of the viral genome into the host. These essential processes are often mediated by proteinaceous complexes that interrupt the shell’s icosahedral symmetry, providing a gateway through the capsid. In this review, we take an inventory of molecular structures observed either internally, or at the 5-fold vertices of icosahedral DNA viruses that infect bacteria, archea and eukaryotes. Taking advantage of the recent revolution in cryo-electron microscopy (cryo-EM) and building upon a wealth of crystallographic structures of individual components, we review the design principles of non-icosahedral structural components that interrupt icosahedral symmetry and discuss how these macromolecules play vital roles in genome packaging, ejection and host receptor-binding. Full article
(This article belongs to the Special Issue Advances in Structural Virology via Cryo-EM)
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Graphical abstract

9 pages, 1624 KiB  
Review
Geometric Defects and Icosahedral Viruses
by Joseph Che-Yen Wang, Suchetana Mukhopadhyay and Adam Zlotnick
Viruses 2018, 10(1), 25; https://doi.org/10.3390/v10010025 - 4 Jan 2018
Cited by 21 | Viewed by 6991
Abstract
We propose that viruses with geometric defects are not necessarily flawed viruses. A geometric defect may be a reactive site. Defects may facilitate assembly, dissociation, or accessibility of cellular proteins to virion components. In single molecule studies of hepadnavirus assembly, defects and overgrowth [...] Read more.
We propose that viruses with geometric defects are not necessarily flawed viruses. A geometric defect may be a reactive site. Defects may facilitate assembly, dissociation, or accessibility of cellular proteins to virion components. In single molecule studies of hepadnavirus assembly, defects and overgrowth are common features. Icosahedral alphaviruses and flaviviruses, among others, have capsids with geometric defects. Similarly, immature retroviruses, which are non-icosahedral, have numerous “errors”. In many viruses, asymmetric exposure of interior features allows for regulated genome release or supports intracellular trafficking. In these viruses, the defects likely serve a biological function. Commonly used approaches for spherical virus structure determination use symmetry averaging, which obscures defects. We suggest that there are three classes of asymmetry: regular asymmetry as might be found in a tailed phage, irregular asymmetry as found, for example, in defects randomly trapped during assembly, and dynamic asymmetry due to Brownian dynamics of virus capsids. Awareness of their presence and recent advances in electron microscopy will allow unprecedented investigation of capsid irregularities to investigate their biological relevance. Full article
(This article belongs to the Special Issue Advances in Structural Virology via Cryo-EM)
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