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Yorodumi- EMDB-6001: Fako virus capsid: a newly-isolated reovirus has the simplest gen... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6001 | |||||||||
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Title | Fako virus capsid: a newly-isolated reovirus has the simplest genomic and structural organization of any reovirus | |||||||||
Map data | Single-particle reconstruction of Fako virus genome-free capsids | |||||||||
Sample |
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Keywords | virus / Reoviridae / Spinareovirinae / Dinovernavirus / Fako virus / FAKV / dsRNA virus / invertebrate virus / reovirus / Aedes / dsRNA | |||||||||
Function / homology | Function and homology information : / : / : / : / Reovirus VP3 protein, guanylyltransferase (GTase) / Reovirus turret protein, bridge domain / Reovirus VP3 protein, Methyltransferase domain 1 / Reovirus VP3 protein, Methyltransferase domain 2 / : / Inner layer core protein VP1-like, C-terminal Similarity search - Domain/homology | |||||||||
Biological species | Fako virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.8 Å | |||||||||
Authors | Auguste AJ / Kaelber JT / Fokam EB / Guzman H / Carrington CVF / Erasmus JH / Kamgang B / Popov VL / Jakana J / Liu X ...Auguste AJ / Kaelber JT / Fokam EB / Guzman H / Carrington CVF / Erasmus JH / Kamgang B / Popov VL / Jakana J / Liu X / Wood TG / Widen SG / Vasilakis N / Tesh RB / Chiu W / Weaver SC | |||||||||
Citation | Journal: J Virol / Year: 2015 Title: A newly isolated reovirus has the simplest genomic and structural organization of any reovirus. Authors: Albert J Auguste / Jason T Kaelber / Eric B Fokam / Hilda Guzman / Christine V F Carrington / Jesse H Erasmus / Basile Kamgang / Vsevolod L Popov / Joanita Jakana / Xiangan Liu / Thomas G ...Authors: Albert J Auguste / Jason T Kaelber / Eric B Fokam / Hilda Guzman / Christine V F Carrington / Jesse H Erasmus / Basile Kamgang / Vsevolod L Popov / Joanita Jakana / Xiangan Liu / Thomas G Wood / Steven G Widen / Nikos Vasilakis / Robert B Tesh / Wah Chiu / Scott C Weaver / Abstract: A total of 2,691 mosquitoes representing 17 species was collected from eight locations in southwest Cameroon and screened for pathogenic viruses. Ten isolates of a novel reovirus (genus ...A total of 2,691 mosquitoes representing 17 species was collected from eight locations in southwest Cameroon and screened for pathogenic viruses. Ten isolates of a novel reovirus (genus Dinovernavirus) were detected by culturing mosquito pools on Aedes albopictus (C6/36) cell cultures. A virus that caused overt cytopathic effects was isolated, but it did not infect vertebrate cells or produce detectable disease in infant mice after intracerebral inoculation. The virus, tentatively designated Fako virus (FAKV), represents the first 9-segment, double-stranded RNA (dsRNA) virus to be isolated in nature. FAKV appears to have a broad mosquito host range, and its detection in male specimens suggests mosquito-to-mosquito transmission in nature. The structure of the T=1 FAKV virion, determined to subnanometer resolution by cryoelectron microscopy (cryo-EM), showed only four proteins per icosahedral asymmetric unit: a dimer of the major capsid protein, one turret protein, and one clamp protein. While all other turreted reoviruses of known structures have at least two copies of the clamp protein per asymmetric unit, FAKV's clamp protein bound at only one conformer of the major capsid protein. The FAKV capsid architecture and genome organization represent the most simplified reovirus described to date, and phylogenetic analysis suggests that it arose from a more complex ancestor by serial loss-of-function events. IMPORTANCE: We describe the detection, genetic, phenotypic, and structural characteristics of a novel Dinovernavirus species isolated from mosquitoes collected in Cameroon. The virus, tentatively ...IMPORTANCE: We describe the detection, genetic, phenotypic, and structural characteristics of a novel Dinovernavirus species isolated from mosquitoes collected in Cameroon. The virus, tentatively designated Fako virus (FAKV), is related to both single-shelled and partially double-shelled viruses. The only other described virus in this genus was isolated from cultured mosquito cells. It was previously unclear whether the phenotypic characteristics of that virus were reflective of this genus in nature or were altered during serial passaging in the chronically infected cell line. FAKV is a naturally occurring single-shelled reovirus with a unique virion architecture that lacks several key structural elements thought to stabilize a single-shelled reovirus virion, suggesting what may be the minimal number of proteins needed to form a viable reovirus particle. FAKV evolved from more complex ancestors by losing a genome segment and several virion proteins. | |||||||||
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_6001.map.gz | 115.2 MB | EMDB map data format | |
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Header (meta data) | emd-6001-v30.xml emd-6001.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | emd_6001.png | 349.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6001 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6001 | HTTPS FTP |
-Validation report
Summary document | emd_6001_validation.pdf.gz | 79.2 KB | Display | EMDB validaton report |
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Full document | emd_6001_full_validation.pdf.gz | 78.3 KB | Display | |
Data in XML | emd_6001_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6001 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6001 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6001.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Single-particle reconstruction of Fako virus genome-free capsids | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.78 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 : Fako virus genome-free capsid
Entire | Name: Fako virus genome-free capsid |
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Components |
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-Supramolecule #1000: Fako virus genome-free capsid
Supramolecule | Name: Fako virus genome-free capsid / type: sample / ID: 1000 / Details: The sample was derived from whole virions. Oligomeric state: icosahedral capsid of 60 asymmetric units with 4 proteins each Number unique components: 1 |
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Molecular weight | Theoretical: 25 MDa |
-Supramolecule #1: Fako virus
Supramolecule | Name: Fako virus / type: virus / ID: 1 / Sci species name: Fako virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Aedes albopictus (Asian tiger mosquito) / synonym: INVERTEBRATES |
Host system | Organism: Aedes aegypti (yellow fever mosquito) / Recombinant cell: C6/36 |
Molecular weight | Theoretical: 25 MDa |
Virus shell | Shell ID: 1 / Diameter: 580 Å / T number (triangulation number): 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 / Details: 10 mM Tris-HCl, 1 mM EDTA, 0.1 M NaCl |
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Grid | Details: 200 mesh copper Quantifoil R 2/2, glow discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 3.5 seconds. |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Temperature | Average: 86.5 K |
Alignment procedure | Legacy - Astigmatism: Objective lens twofold astigmatism was corrected. |
Specialist optics | Energy filter - Name: Omega filter |
Details | Damage correction and motion correction was performed. |
Date | Dec 12, 2013 |
Image recording | Category: CCD / Film or detector model: OTHER / Number real images: 71 / Average electron dose: 40 e/Å2 / Bits/pixel: 32 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 22964 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal magnification: 20000 |
Sample stage | Specimen holder model: JEOL 3200FSC CRYOHOLDER |
-Image processing
CTF correction | Details: CTF fit for each frame, corrected for each particle |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: OTHER / Software - Name: MPSA, EMAN2 / Number images used: 1385 |