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      Virion Structure of Black Queen Cell Virus, a Common Honeybee Pathogen

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          ABSTRACT

          Viral diseases are a major threat to honeybee ( Apis mellifera) populations worldwide and therefore an important factor in reliable crop pollination and food security. Black queen cell virus (BQCV) is the etiological agent of a fatal disease of honeybee queen larvae and pupae. The virus belongs to the genus Triatovirus from the family Dicistroviridae, which is part of the order Picornavirales. Here we present a crystal structure of BQCV determined to a resolution of 3.4 Å. The virion is formed by 60 copies of each of the major capsid proteins VP1, VP2, and VP3; however, there is no density corresponding to a 75-residue-long minor capsid protein VP4 encoded by the BQCV genome. We show that the VP4 subunits are present in the crystallized virions that are infectious. This aspect of the BQCV virion is similar to that of the previously characterized triatoma virus and supports the recent establishment of the separate genus Triatovirus within the family Dicistroviridae. The C terminus of VP1 and CD loops of capsid proteins VP1 and VP3 of BQCV form 34-Å-tall finger-like protrusions at the virion surface. The protrusions are larger than those of related dicistroviruses.

          IMPORTANCE The western honeybee is the most important pollinator of all, and it is required to sustain the agricultural production and biodiversity of wild flowering plants. However, honeybee populations worldwide are suffering from virus infections that cause colony losses. One of the most common, and least known, honeybee pathogens is black queen cell virus (BQCV), which at high titers causes queen larvae and pupae to turn black and die. Here we present the three-dimensional virion structure of BQCV, determined by X-ray crystallography. The structure of BQCV reveals large protrusions on the virion surface. Capsid protein VP1 of BQCV does not contain a hydrophobic pocket. Therefore, the BQCV virion structure provides evidence that capsid-binding antiviral compounds that can prevent the replication of vertebrate picornaviruses may be ineffective against honeybee virus infections.

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          Multiple sequence alignment with the Clustal series of programs.

          R Chenna (2003)
          The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the robustness, portability and user-friendliness of the programs. New features include NEXUS and FASTA format output, printing range numbers and faster tree calculation. Although, Clustal was originally developed to run on a local computer, numerous Web servers have been set up, notably at the EBI (European Bioinformatics Institute) (http://www.ebi.ac.uk/clustalw/).
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            Version 1.2 of the Crystallography and NMR system.

            Version 1.2 of the software system, termed Crystallography and NMR system (CNS), for crystallographic and NMR structure determination has been released. Since its first release, the goals of CNS have been (i) to create a flexible computational framework for exploration of new approaches to structure determination, (ii) to provide tools for structure solution of difficult or large structures, (iii) to develop models for analyzing structural and dynamical properties of macromolecules and (iv) to integrate all sources of information into all stages of the structure determination process. Version 1.2 includes an improved model for the treatment of disordered solvent for crystallographic refinement that employs a combined grid search and least-squares optimization of the bulk solvent model parameters. The method is more robust than previous implementations, especially at lower resolution, generally resulting in lower R values. Other advances include the ability to apply thermal factor sharpening to electron density maps. Consistent with the modular design of CNS, these additions and changes were implemented in the high-level computing language of CNS.
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              Improved methods for building protein models in electron density maps and the location of errors in these models.

              Map interpretation remains a critical step in solving the structure of a macromolecule. Errors introduced at this early stage may persist throughout crystallographic refinement and result in an incorrect structure. The normally quoted crystallographic residual is often a poor description for the quality of the model. Strategies and tools are described that help to alleviate this problem. These simplify the model-building process, quantify the goodness of fit of the model on a per-residue basis and locate possible errors in peptide and side-chain conformations.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                J Virol
                J. Virol
                jvi
                jvi
                JVI
                Journal of Virology
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                0022-538X
                1098-5514
                11 January 2017
                28 February 2017
                15 March 2017
                28 February 2017
                : 91
                : 6
                : e02100-16
                Affiliations
                [a ]Structural Virology, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
                [b ]Department of Zoology, Fishery, Hydrobiology, and Apidology, Faculty of Agronomy, Mendel University in Brno, Brno, Czech Republic
                [c ]Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
                Hudson Institute of Medical Research
                Author notes
                Address correspondence to Pavel Plevka, pavel.plevka@ 123456ceitec.muni.cz .
                [*]

                Present address: Hoa Khanh Tran Kiem, Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.

                Citation Spurny R, Přidal A, Pálková L, Kiem HKT, de Miranda JR, Plevka P. 2017. Virion structure of black queen cell virus, a common honeybee pathogen. J Virol 91:e02100-16. https://doi.org/10.1128/JVI.02100-16.

                Article
                02100-16
                10.1128/JVI.02100-16
                5331821
                28077635
                cc7fff04-9b6f-4ce1-92e5-caba2440a39d
                Copyright © 2017 Spurny et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 10 October 2016
                : 21 December 2016
                Page count
                supplementary-material: 1, Figures: 9, Tables: 2, Equations: 0, References: 76, Pages: 14, Words: 9124
                Funding
                Funded by: European Research Council
                Award ID: 355855
                Award Recipient : Pavel Plevka
                Funded by: European Molecular Biology Organization (EMBO) https://doi.org/10.13039/100004410
                Award ID: 3041
                Award Recipient : Pavel Plevka
                Funded by: Ministerstvo Školství, Mládeže a Tělovýchovy (MŠMT) https://doi.org/10.13039/501100001823
                Award ID: LQ1601
                Categories
                Structure and Assembly
                Custom metadata
                March 2017

                Microbiology & Virology
                virus,apis mellifera,honey bee,honeybee,picornavirales,dicistroviridae,cripavirus,triatovirus,virion,structure,x ray,crystallography,capsid,insect disease,x-ray crystallography

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