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- EMDB-9619: Cyro-EM structure of DNA-full Medusavirus -

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Basic information

Entry
Database: EMDB / ID: EMD-9619
TitleCyro-EM structure of DNA-full Medusavirus
Map dataCryo-EM structure of DNA-full Medusavirus
Sample
  • Virus: Medusavirus
Biological speciesMedusavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 31.8 Å
AuthorsYoshikawa G / Blanc-Mathieu R / Song C / Kayama Y / Mochizuki T / Murata K / Ogata H / Takemura M
CitationJournal: J Virol / Year: 2019
Title: Medusavirus, a Novel Large DNA Virus Discovered from Hot Spring Water.
Authors: Genki Yoshikawa / Romain Blanc-Mathieu / Chihong Song / Yoko Kayama / Tomohiro Mochizuki / Kazuyoshi Murata / Hiroyuki Ogata / Masaharu Takemura /
Abstract: Recent discoveries of new large DNA viruses reveal high diversity in their morphologies, genetic repertoires, and replication strategies. Here, we report the novel features of medusavirus, a large ...Recent discoveries of new large DNA viruses reveal high diversity in their morphologies, genetic repertoires, and replication strategies. Here, we report the novel features of medusavirus, a large DNA virus newly isolated from hot spring water in Japan. Medusavirus, with a diameter of 260 nm, shows a T=277 icosahedral capsid with unique spherical-headed spikes on its surface. It has a 381-kb genome encoding 461 putative proteins, 86 of which have their closest homologs in , whereas 279 (61%) are orphan genes. The virus lacks the genes encoding DNA topoisomerase II and RNA polymerase, showing that DNA replication takes place in the host nucleus, whereas the progeny virions are assembled in the cytoplasm. Furthermore, the medusavirus genome harbored genes for all five types of histones (H1, H2A, H2B, H3, and H4) and one DNA polymerase, which are phylogenetically placed at the root of the eukaryotic clades. In contrast, the host amoeba encoded many medusavirus homologs, including the major capsid protein. These facts strongly suggested that amoebae are indeed the most promising natural hosts of medusavirus, and that lateral gene transfers have taken place repeatedly and bidirectionally between the virus and its host since the early stage of their coevolution. Medusavirus reflects the traces of direct evolutionary interactions between the virus and eukaryotic hosts, which may be caused by sharing the DNA replication compartment and by evolutionarily long lasting virus-host relationships. Based on its unique morphological characteristics and phylogenomic relationships with other known large DNA viruses, we propose that medusavirus represents a new family, We have isolated a new nucleocytoplasmic large DNA virus (NCLDV) from hot spring water in Japan, named medusavirus. This new NCLDV is phylogenetically placed at the root of the eukaryotic clades based on the phylogenies of several key genes, including that encoding DNA polymerase, and its genome surprisingly encodes the full set of histone homologs. Furthermore, its laboratory host, , encodes many medusavirus homologs in its genome, including the major capsid protein, suggesting that the amoeba is the genuine natural host from ancient times of this newly described virus and that lateral gene transfers have repeatedly occurred between the virus and amoeba. These results suggest that medusavirus is a unique NCLDV preserving ancient footprints of evolutionary interactions with its hosts, thus providing clues to elucidate the evolution of NCLDVs, eukaryotes, and virus-host interaction. Based on the dissimilarities with other known NCLDVs, we propose that medusavirus represents a new viral family, .
History
DepositionAug 15, 2018-
Header (metadata) releaseFeb 6, 2019-
Map releaseFeb 6, 2019-
UpdateApr 24, 2019-
Current statusApr 24, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9619.png

Downloads & links

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Map

FileDownload / File: emd_9619.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of DNA-full Medusavirus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.32 Å/pix.
x 400 pix.
= 2928. Å		7.32 Å/pix.
x 400 pix.
= 2928. Å		7.32 Å/pix.
x 400 pix.
= 2928. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.08323174 - 0.20813248
Average (Standard dev.)0.013311595 (±0.028356452)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 2928.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.327.327.32
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z2928.0002928.0002928.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0830.2080.013

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Supplemental data

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Sample components

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Entire : Medusavirus

EntireName: Medusavirus
Components
  • Virus: Medusavirus

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Supramolecule #1: Medusavirus

SupramoleculeName: Medusavirus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 32644 / Sci species name: Medusavirus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Acanthamoeba castellanii (eukaryote)
Virus shellShell ID: 1 / Diameter: 2600.0 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
Sugar embeddingMaterial: amorphous ice
GridModel: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL 2200FS
TemperatureMin: 76.0 K / Max: 77.0 K
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Digitization - Dimensions - Width: 5120 pixel / Digitization - Dimensions - Height: 3840 pixel / Digitization - Sampling interval: 6.4 µm / Digitization - Frames/image: 3-75 / Number real images: 1198 / Average exposure time: 3.0 sec. / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 40.0 µm / Calibrated defocus max: 4.9672 µm / Calibrated defocus min: 1.5783 µm / Calibrated magnification: 27862 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 25000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 31.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 2880
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final 3D classificationSoftware - Name: RELION (ver. 2.0)

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