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- EMDB-64895: Ushikuvirus (9.3A cryo-EM map) -

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Basic information

Entry
Database: EMDB / ID: EMD-64895
TitleUshikuvirus (9.3A cryo-EM map)
Map dataUshikuvirus (Postprocessed map, Ewald sphere corrected)
Sample
  • Virus: Ushikuvirus sp.
KeywordsGiant virus / Virus / Ushikuvirus
Biological speciesUshikuvirus sp.
Methodsingle particle reconstruction / cryo EM / Resolution: 9.3 Å
AuthorsBurton-Smith RN / Murata K
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H03078 Japan
Other government22EXC601-4 Japan
CitationJournal: J Virol / Year: 2025
Title: A newly isolated giant virus, ushikuvirus, is closely related to clandestinovirus and shows a unique capsid surface structure and host cell interactions.
Authors: Jiwan Bae / Narumi Hatori / Raymond N Burton-Smith / Kazuyoshi Murata / Masaharu Takemura /
Abstract: The family , assigned in 2023, consists of three strains of medusavirus that infect acanthamoeba. A closely related species, clandestinovirus, which infects vermamoeba, was reported in 2021. Here, we ...The family , assigned in 2023, consists of three strains of medusavirus that infect acanthamoeba. A closely related species, clandestinovirus, which infects vermamoeba, was reported in 2021. Here, we report a newly identified clandestinovirus-like virus, named ushikuvirus, isolated from a freshwater pond in Japan. The ushikuvirus genome was at least 666,605 bp and contained 784 genes. Annotation revealed that a substantial proportion (58%) of open reading frames (ORFs) are ORFans, and 25% of ORFs are similar to those of other viruses in the phylum . Among ORFs sharing sequence similarity with other viruses, a large proportion (80%) were similar to the clandestinovirus sequences. However, ushikuvirus shows several remarkable features. (i) The capsid surface has multiple spike-like "cap" structures, some of which exhibit a fibrous structure. (ii) The infection cycle is longer than that of medusavirus and clandestinovirus, and the virus exhibits a unique cytopathic effect (CPE) that causes enlargement of host vermamoeba cells. (iii) The virus forms a viral factory for duplication and destroys the nuclear membrane of vermamoeba cells, a phenomenon not observed with medusavirus and clandestinovirus. These characteristics indicate that this newly isolated giant virus related to the family and Clandestinovirus may represent a key taxon for elucidating virus-host interactions and the evolution of this virus group.IMPORTANCEThe family consists of only one genus, including three species: , , and the recently described medusavirus euryale. These three medusaviruses have been reported to infect . Meanwhile, clandestinovirus, a closely related species in the family , infects vermamoeba. In these viruses, genome replication takes place in the nucleus of the host cell, and like eukaryotes, the genome encodes a full set of histones and has numerous spikes on the capsid surface. Here, we report a new member of this unique virus group, ushikuvirus, which displays distinct features including cytopathic effects in vermamoeba cells. These findings improve our understanding of the biological significance of the family and closely related taxa and provide a basis for elucidating the evolutionary relationships of giant viruses with their eukaryotic hosts.
History
DepositionJun 2, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64895.png

Downloads & links

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Map

FileDownload / File: emd_64895.map.gz / Format: CCP4 / Size: 4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUshikuvirus (Postprocessed map, Ewald sphere corrected)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.87 Å/pix.
x 1024 pix.
= 2936.832 Å		2.87 Å/pix.
x 1024 pix.
= 2936.832 Å		2.87 Å/pix.
x 1024 pix.
= 2936.832 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.868 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00555
Minimum - Maximum-0.007091286 - 0.016155714
Average (Standard dev.)0.0009372766 (±0.0027747366)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions102410241024
Spacing102410241024
CellA=B=C: 2936.832 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Ushikuvirus (Half map 2, Ewald sphere corrected)

Fileemd_64895_additional_1.map
AnnotationUshikuvirus (Half map 2, Ewald sphere corrected)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Ushikuvirus (Half map 1, Ewald sphere corrected)

Fileemd_64895_half_map_1.map
AnnotationUshikuvirus (Half map 1, Ewald sphere corrected)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Ushikuvirus (Postprocessed map (masked), Ewald sphere corrected)

Fileemd_64895_half_map_2.map
AnnotationUshikuvirus (Postprocessed map (masked), Ewald sphere corrected)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ushikuvirus sp.

EntireName: Ushikuvirus sp.
Components
  • Virus: Ushikuvirus sp.

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Supramolecule #1: Ushikuvirus sp.

SupramoleculeName: Ushikuvirus sp. / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 3385543 / Sci species name: Ushikuvirus sp. / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 8.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio model from 2D classes
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1600
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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