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- EMDB-39298: 2-fold block of DNA-Empty medusavirus capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-39298
Title2-fold block of DNA-Empty medusavirus capsid
Map data2-fold block of DNA-Empty medusavirus capsid
Sample
  • Virus: Acanthamoeba castellanii medusavirus
KeywordsGiant virus / NCLDV / Icosahedral / VIRUS
Biological speciesAcanthamoeba castellanii medusavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 9.88 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: 2024
Title: Subnanometer structure of medusavirus capsid during maturation using cryo-electron microscopy.
Authors: Ryoto Watanabe / Chihong Song / Masaharu Takemura / Kazuyoshi Murata /
Abstract: Medusavirus is a giant virus classified into an independent family of . Amoebae infected with medusavirus release immature particles in addition to virions. These particles were suggested to exhibit ...Medusavirus is a giant virus classified into an independent family of . Amoebae infected with medusavirus release immature particles in addition to virions. These particles were suggested to exhibit the maturation process of this virus, but the structure of these capsids during maturation remains unknown. Here, we apply a block-based reconstruction method in cryo-electron microscopy (cryo-EM) single particle analysis to these viral capsids, extending the resolution to 7-10 Å. The maps reveal a novel network composed of minor capsid proteins (mCPs) supporting major capsid proteins (MCPs). A predicted molecular model of the MCP fitted into the cryo-EM maps clarified the boundaries between the MCP and the underlining mCPs, as well as between the MCP and the outer spikes, and identified molecular interactions between the MCP and these components. Several structural changes of the mCPs under the fivefold vertices of the immature particles were observed, depending on the presence or absence of the underlying internal membrane. In addition, the lower part of the penton proteins on the fivefold vertices was also missing in mature virions. These dynamic conformational changes of mCPs indicate an important function in the maturation process of medusavirus.IMPORTANCEThe structural changes of giant virus capsids during maturation have not thus far been well clarified. Medusavirus is a unique giant virus in which infected amoebae release immature particles in addition to mature virus particles. In this study, we used cryo-electron microscopy to investigate immature and mature medusavirus particles and elucidate the structural changes of the viral capsid during the maturation process. In DNA-empty particles, the conformation of the minor capsid proteins changed dynamically depending on the presence or absence of the underlying internal membranes. In DNA-full particles, the lower part of the penton proteins was lost. This is the first report of structural changes of the viral capsid during the maturation process of giant viruses.
History
DepositionFeb 28, 2024-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39298.png

Downloads & links

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Map

FileDownload / File: emd_39298.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation2-fold block of DNA-Empty medusavirus capsid
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.03 Å/pix.
x 512 pix.
= 1551.36 Å		3.03 Å/pix.
x 512 pix.
= 1551.36 Å		3.03 Å/pix.
x 512 pix.
= 1551.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0151
Minimum - Maximum-0.12337213 - 0.18254445
Average (Standard dev.)0.00020894122 (±0.0075634643)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 1551.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39298_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39298_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: No
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
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 249300
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 208834
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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