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Cryo-EM structure of a Marseilleviridae virus particle reveals a large internal microassembly
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
National Institute for Physiological Sciences (NIPS), Okazaki, Aichi, 444-8585 Japan.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
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2018 (English)In: Virology, ISSN 0042-6822, E-ISSN 1096-0341, Vol. 516, p. 239-245, article id S0042-6822(18)30028-XArticle in journal (Refereed) Published
Abstract [en]

Nucleocytoplasmic large DNA viruses (NCLDVs) blur the line between viruses and cells. Melbournevirus (MelV, family Marseilleviridae) belongs to a new family of NCLDVs. Here we present an electron cryo-microscopy structure of the MelV particle, with the large triangulation number T = 309 constructed by 3080 pseudo-hexagonal capsomers. The most distinct feature of the particle is a large and dense body (LDB) consistently found inside all particles. Electron cryo-tomography of 147 particles shows that the LDB is preferentially located in proximity to the probable lipid bilayer. The LDB is 30 nm in size and its density matches that of a genome/protein complex. The observed LDB reinforces the structural complexity of MelV, setting it apart from other NCLDVs.

Place, publisher, year, edition, pages
2018. Vol. 516, p. 239-245, article id S0042-6822(18)30028-X
Keywords [en]
Amoeba, Capsid, Cryo-electron microscopy, Marseilleviridae, Melbournevirus, NCLDV, Protein complex, Structure, Tomography, Virus
National Category
Biophysics
Identifiers
URN: urn:nbn:se:uu:diva-370071DOI: 10.1016/j.virol.2018.01.021ISI: 000428004800025PubMedID: 29407382OAI: oai:DiVA.org:uu-370071DiVA, id: diva2:1272303
Funder
Swedish Research Council, 628-20081109 822-2010-6157 822-2012-5260 828-2012-108Knut and Alice Wallenberg Foundation, KAW-2011.081EU, European Research Council, ERC-291602The Swedish Foundation for International Cooperation in Research and Higher Education (STINT), JA2014-5721Available from: 2018-12-18 Created: 2018-12-18 Last updated: 2019-08-25Bibliographically approved
In thesis
1. Structural Studies of Large dsDNA Viruses using Single Particle Methods
Open this publication in new window or tab >>Structural Studies of Large dsDNA Viruses using Single Particle Methods
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Structural studies of large biological assemblies pose a unique problem due to their size, complexity and heterogeneity. Conventional methods like x-ray crystallography, NMR, etc. are limited in their ability to address these issues. To overcome some of these limitations, single particle methods were used. In these methods, each particle image is manipulated individually to find the best possible set of images to reconstruct the 3D structure. The structural studies in this thesis, exploit the advantages of single particle methods. 

The large data set generated by the SPI study of PR772 provides better statistics about the sample quality due to the use of GDVN, a container-free sample delivery method. By analyzing the diffusion map, we see that the use of GDVNs as a sample delivery method produces wide range of particle sizes owing to the large droplet that are created. 

The high-resolution structure of bacteriophage PR772 confirmed the speculation about the heteropentameric nature of the penton and revealed the new architecture of the vertex complex consisting of a hetero-pentameric penton formed with three copies of P5 and two copies of P31. The beta propeller region of P2, formed by domains I and II is bound to the N-terminal domain of P5. The structure also reveals new conformations of N-terminal and C-terminal region of P3 which play an important role in particle assembly and structural stability. 

The study of Melbournevirus revealed the protein composition in a packed particle. The CryoEM structure of Melbournevirus reveals a T=309 capsid with an inner lipid membrane. A dense body was found in the viral particle, a feature not observed in other viruses of the Marseilleviridae family. The density of this body is similar to a nucleic acid-protein complex. This observation, along with the histone-like protein identified during study, suggest genome organization in the viral particle, similar to higher organisms.

The soft X-ray microscope operated in the water-window shows the progression of the Cedratvirus lurbo infection in the host cell without the use of chemical fixation, staining, sample dehydration or polymer embedding. The study revealed a significant bioconversion from the host cell to the viral particle at later stages of infection.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2019. p. 72
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1847
Keywords
PR772, phage, PRD1, Bacteriophage, coliphage, Melbournevirus, Cedratvirus, lurbo, Pithovirus, CryoEM, Single particle imaging, Coherent, Diffractive, Imaging, Soft X-ray, Microscopy, Microscope, GDVN, High resolution, XFEL, aerosol, Injection, electrospray, gas dynamic virtual nozzle, CDI, CXI, FEL
National Category
Structural Biology Biophysics
Research subject
Chemistry with specialization in Biophysics
Identifiers
urn:nbn:se:uu:diva-391671 (URN)978-91-513-0732-9 (ISBN)
Public defence
2019-10-11, Room C2:301, BMC, Husargatan 3, Uppsala, 13:00 (English)
Opponent
Supervisors
Available from: 2019-09-20 Created: 2019-08-25 Last updated: 2019-10-15

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Okamoto, KentaReddy, Hemanth K.N.Maia, Filipe R.N.C.Larsson, Daniel S DHajdu, JanosSvenda, Martin

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