+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9619 | |||||||||
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Title | Cyro-EM structure of DNA-full Medusavirus | |||||||||
Map data | Cryo-EM structure of DNA-full Medusavirus | |||||||||
Sample |
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Biological species | Medusavirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 31.8 Å | |||||||||
Authors | Yoshikawa G / Blanc-Mathieu R / Song C / Kayama Y / Mochizuki T / Murata K / Ogata H / Takemura M | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9619.map.gz | 219 MB | EMDB map data format | |
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Header (meta data) | emd-9619-v30.xml emd-9619.xml | 12.2 KB 12.2 KB | Display Display | EMDB header |
Images | emd_9619.png | 129.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9619 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9619 | HTTPS FTP |
-Validation report
Summary document | emd_9619_validation.pdf.gz | 78.6 KB | Display | EMDB validaton report |
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Full document | emd_9619_full_validation.pdf.gz | 77.7 KB | Display | |
Data in XML | emd_9619_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9619 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9619 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9619.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of DNA-full Medusavirus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 7.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Medusavirus
Entire | Name: Medusavirus |
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Components |
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-Supramolecule #1: Medusavirus
Supramolecule | Name: 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 |
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Host (natural) | Organism: Acanthamoeba castellanii (eukaryote) |
Virus shell | Shell ID: 1 / Diameter: 2600.0 Å / T number (triangulation number): 277 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Sugar embedding | Material: amorphous ice |
Grid | Model: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | JEOL 2200FS |
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Temperature | Min: 76.0 K / Max: 77.0 K |
Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Image recording | Film 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 beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |