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Yorodumi- EMDB-3823: Structure of the truncated African cichlid nackednavirus icosahed... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3823 | |||||||||
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Title | Structure of the truncated African cichlid nackednavirus icosahedral capsid | |||||||||
Map data | Structure of the truncated African cichlid nackednavirus capsid | |||||||||
Sample |
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Biological species | Retro-transcribing viruses | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.0 Å | |||||||||
Authors | Mattei S / Briggs JAG / Seitz S | |||||||||
Citation | Journal: Cell Host Microbe / Year: 2017 Title: Deciphering the Origin and Evolution of Hepatitis B Viruses by Means of a Family of Non-enveloped Fish Viruses. Authors: Chris Lauber / Stefan Seitz / Simone Mattei / Alexander Suh / Jürgen Beck / Jennifer Herstein / Jacob Börold / Walter Salzburger / Lars Kaderali / John A G Briggs / Ralf Bartenschlager / Abstract: Hepatitis B viruses (HBVs), which are enveloped viruses with reverse-transcribed DNA genomes, constitute the family Hepadnaviridae. An outstanding feature of HBVs is their streamlined genome ...Hepatitis B viruses (HBVs), which are enveloped viruses with reverse-transcribed DNA genomes, constitute the family Hepadnaviridae. An outstanding feature of HBVs is their streamlined genome organization with extensive gene overlap. Remarkably, the ∼1,100 bp open reading frame (ORF) encoding the envelope proteins is fully nested within the ORF of the viral replicase P. Here, we report the discovery of a diversified family of fish viruses, designated nackednaviruses, which lack the envelope protein gene, but otherwise exhibit key characteristics of HBVs including genome replication via protein-primed reverse-transcription and utilization of structurally related capsids. Phylogenetic reconstruction indicates that these two virus families separated more than 400 million years ago before the rise of tetrapods. We show that HBVs are of ancient origin, descending from non-enveloped progenitors in fishes. Their envelope protein gene emerged de novo, leading to a major transition in viral lifestyle, followed by co-evolution with their hosts over geologic eras. | |||||||||
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_3823.map.gz | 474.5 MB | EMDB map data format | |
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Header (meta data) | emd-3823-v30.xml emd-3823.xml | 12.2 KB 12.2 KB | Display Display | EMDB header |
Images | emd_3823.png | 102.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3823 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3823 | HTTPS FTP |
-Validation report
Summary document | emd_3823_validation.pdf.gz | 240.6 KB | Display | EMDB validaton report |
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Full document | emd_3823_full_validation.pdf.gz | 239.7 KB | Display | |
Data in XML | emd_3823_validation.xml.gz | 8.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3823 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3823 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3823.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of the truncated African cichlid nackednavirus capsid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.18 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 : Retro-transcribing viruses
Entire | Name: Retro-transcribing viruses |
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Components |
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-Supramolecule #1: Retro-transcribing viruses
Supramolecule | Name: Retro-transcribing viruses / type: virus / ID: 1 / Parent: 0 Details: truncated capsid variant (aa 1-146) lacking the C-terminal nucleic acid binding domain. NCBI-ID: 35268 / Sci species name: Retro-transcribing viruses / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Ophthalmotilapia ventralis (fish) |
Host system | Organism: Escherichia coli (E. coli) |
Virus shell | Shell ID: 1 / Name: capsid / Diameter: 320.0 Å / T number (triangulation number): 3 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Grid | Model: Protochips C-Flat / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: 20 mA |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 1-7 / Number grids imaged: 1 / Number real images: 1018 / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |