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- EMDB-32072: Cryo-EM structure of Empty medusavirus particle -

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Basic information

Entry
Database: EMDB / ID: EMD-32072
TitleCryo-EM structure of Empty medusavirus particle
Map dataCryo-EM 3D reconstruction of Empty medusavirus particle.
Sample
  • Virus: Acanthamoeba castellanii medusavirus
KeywordsGiant virus / NCLDV / Icosahedral / VIRUS
Biological speciesAcanthamoeba castellanii medusavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 21.5 Å
AuthorsMurata K / Song C / Watanabe R
Funding support Japan, 4 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP17H05825 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP19H04845 Japan
Japan Society for the Promotion of Science (JSPS)20H03078 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101072 Japan
CitationJournal: J Virol / Year: 2022
Title: Particle Morphology of Medusavirus Inside and Outside the Cells Reveals a New Maturation Process of Giant Viruses.
Authors: Ryoto Watanabe / Chihong Song / Yoko Kayama / Masaharu Takemura / Kazuyoshi Murata /
Abstract: Medusavirus, a giant virus, is phylogenetically closer to eukaryotes than the other giant viruses and has been recently classified as an independent species. However, details of its morphology and ...Medusavirus, a giant virus, is phylogenetically closer to eukaryotes than the other giant viruses and has been recently classified as an independent species. However, details of its morphology and maturation process in host cells remain unclear. Here, we investigated the particle morphology of medusavirus inside and outside infected cells using conventional transmission electron microscopy (C-TEM) and cryo-electron microscopy (cryo-EM). The C-TEM of amoebae infected with the medusavirus showed four types of particles, i.e., pseudo-DNA-empty (p-Empty), DNA-empty (Empty), semi-DNA-full (s-Full), and DNA-full (Full). Time-dependent changes in the four types of particles and their intracellular localization suggested a new maturation process for the medusavirus. Viral capsids and viral DNAs are produced independently in the cytoplasm and nucleus, respectively, and only the empty particles located near the host nucleus can incorporate the viral DNA into the capsid. Therefore, all four types of particles were found outside the cells. The cryo-EM of these particles showed that the intact virus structure, covered with three different types of spikes, was preserved among all particle types, although with minor size-related differences. The internal membrane exhibited a structural array similar to that of the capsid, interacted closely with the capsid, and displayed open membrane structures in the Empty and p-Empty particles. The results suggest that these open structures in the internal membrane are used for an exchange of scaffold proteins and viral DNA during the maturation process. This new model of the maturation process of medusavirus provides insight into the structural and behavioral diversity of giant viruses. Giant viruses exhibit diverse morphologies and maturation processes. In this study, medusavirus showed four types of particle morphologies, both inside and outside the infected cells, when propagated in amoeba culture. Time-course analysis and intracellular localization of the medusavirus in the infected cells suggested a new maturation process via the four types of particles. Like the previously reported pandoravirus, the viral DNA of medusavirus is replicated in the host's nucleus. However, viral capsids are produced independently in the host cytoplasm, and only empty capsids near the nucleus can take up viral DNA. As a result, many immature particles were released from the host cell along with the mature particles. The capsid structure is well conserved among the four types of particles, except for the open membrane structures in the empty particles, suggesting that they are used to exchange scaffold proteins for viral DNAs. These findings indicate that medusavirus has a unique maturation process.
History
DepositionOct 18, 2021-
Header (metadata) releaseApr 27, 2022-
Map releaseApr 27, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_32072.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM 3D reconstruction of Empty medusavirus particle.
Voxel sizeX=Y=Z: 6.06 Å
Density
Contour LevelBy AUTHOR: 0.00355
Minimum - Maximum-0.025312852 - 0.04271613
Average (Standard dev.)0.0001633544 (±0.0035526992)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 3102.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Acanthamoeba castellanii medusavirus

EntireName: Acanthamoeba castellanii medusavirus
Components
  • Virus: Acanthamoeba castellanii medusavirus

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Supramolecule #1: Acanthamoeba castellanii medusavirus

SupramoleculeName: Acanthamoeba castellanii medusavirus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 2080449 / Sci species name: Acanthamoeba castellanii medusavirus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Acanthamoeba castellanii (eukaryote)
Virus shellShell ID: 1 / Name: capsid / Diameter: 260.0 Å / T number (triangulation number): 277

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: MOLYBDENUM
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.1 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 76.0 K / Max: 77.0 K
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Number real images: 2084 / Average exposure time: 3.0 sec. / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4625
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 21.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 4551
FSC plot (resolution estimation)

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