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

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Entry
Database: EMDB / ID: 9619
TitleCyro-EM structure of DNA-full Medusavirus
Map dataCryo-EM structure of DNA-full Medusavirus
SampleMedusavirus:
virus
SourceMedusavirus (others)
Methodsingle particle reconstruction / cryo EM / 31.8 Å resolution
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 ORFans. The virus lacking the genes of DNA topoisomerase II and RNA polymerase showed that the DNA replication takes place in the host nucleus while the progeny virions are assembled in the cytoplasm. Furthermore, Medusavirus encoded all of 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. By contrast, the host amoeba encoded many Medusavirus homologs including the major capsid protein. These facts strongly suggested that amoeba is indeed the most promising natural host of Medusavirus, and lateral gene transfers have taken place repeatedly and bidirectionally between the virus and its host since the early stage of their co-evolution. 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 evolutionarily long lasting viral-host relationships. Based on its unique morphological characteristics and phylogenomic relationships with other known large DNA viruses, we propose that Medusavirus forms a new family We have isolated a new NCLDV virus 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 DNA polymerase, and 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 of this new virus from ancient times, and lateral gene transfers have occurred between the virus and amoeba repeatedly. 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 viral-host interaction. Based on the dissimilarities with other known NCLDVs, we propose that Medusavirus forms a new viral family .
DateDeposition: Aug 15, 2018 / Header (metadata) release: Feb 6, 2019 / Map release: Feb 6, 2019 / Last update: Feb 6, 2019

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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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

Fileemd_9619.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
7.32 Å/pix.
= 2928. Å
400 pix
7.32 Å/pix.
= 2928. Å
400 pix
7.32 Å/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
Contour Level:0.045 (by author), 0.045 (movie #1):
Minimum - Maximum-0.08323174 - 0.20813248
Average (Standard dev.)0.013311595 (0.028356452)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin0.00.00.0
Limit399.0399.0399.0
Spacing400400400
CellA=B=C: 2928.0 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ-6-10-25
NX/NY/NZ564636
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 / Number of components: 1

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Component #1: virus, Medusavirus

VirusName: Medusavirus / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
SpeciesSpecies: Medusavirus (others)
Source (natural)Host Species: Acanthamoeba castellanii (eukaryote)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 95 %

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Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 25000.0 X (nominal), 27862.0 X (calibrated) / Cs: 4.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000.0 - 4000.0 nm / Energy filter: In-column Omega Filter
Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: K ( 76.0 - 77.0 K)
CameraDetector: DIRECT ELECTRON DE-20 (5k x 3k)

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Image acquisition

Image acquisitionNumber of digital images: 1198 / Sampling size: 6.4 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 2880
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 31.8 Å / Resolution method: FSC 0.143 CUT-OFF

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