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- EMDB-6001: Fako virus capsid: a newly-isolated reovirus has the simplest gen... -

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Basic information

Entry
Database: EMDB / ID: EMD-6001
TitleFako virus capsid: a newly-isolated reovirus has the simplest genomic and structural organization of any reovirus
Map dataSingle-particle reconstruction of Fako virus genome-free capsids
Sample
  • Sample: Fako virus genome-free capsid
  • Virus: Fako virus
Keywordsvirus / 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
Major capsid protein / Turret protein / Clamp protein
Similarity search - Component
Biological speciesFako virus
Methodsingle particle reconstruction / cryo EM / Resolution: 7.8 Å
AuthorsAuguste 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
CitationJournal: 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
DepositionJul 23, 2014-
Header (metadata) releaseAug 13, 2014-
Map releaseNov 12, 2014-
UpdateDec 24, 2014-
Current statusDec 24, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6001.png

Downloads & links

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Map

FileDownload / File: emd_6001.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSingle-particle reconstruction of Fako virus genome-free capsids
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.78 Å/pix.
x 320 pix.
= 889.6 Å		2.78 Å/pix.
x 320 pix.
= 889.6 Å		2.78 Å/pix.
x 320 pix.
= 889.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-1.18680322 - 2.12791181
Average (Standard dev.)0.02009096 (±0.17021477)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 889.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.782.782.78
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z889.600889.600889.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-1.1872.1280.020

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Supplemental data

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Sample components

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Entire : Fako virus genome-free capsid

EntireName: Fako virus genome-free capsid
Components
  • Sample: Fako virus genome-free capsid
  • Virus: Fako virus

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Supramolecule #1000: Fako virus genome-free capsid

SupramoleculeName: 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
Molecular weightTheoretical: 25 MDa

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Supramolecule #1: Fako virus

SupramoleculeName: 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
Host (natural)Organism: Aedes albopictus (Asian tiger mosquito) / synonym: INVERTEBRATES
Host systemOrganism: Aedes aegypti (yellow fever mosquito) / Recombinant cell: C6/36
Molecular weightTheoretical: 25 MDa
Virus shellShell ID: 1 / Diameter: 580 Å / T number (triangulation number): 1

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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: 7.8 / Details: 10 mM Tris-HCl, 1 mM EDTA, 0.1 M NaCl
GridDetails: 200 mesh copper Quantifoil R 2/2, glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 3.5 seconds.

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Electron microscopy

MicroscopeJEOL 3200FSC
TemperatureAverage: 86.5 K
Alignment procedureLegacy - Astigmatism: Objective lens twofold astigmatism was corrected.
Specialist opticsEnergy filter - Name: Omega filter
DetailsDamage correction and motion correction was performed.
DateDec 12, 2013
Image recordingCategory: CCD / Film or detector model: OTHER / Number real images: 71 / Average electron dose: 40 e/Å2 / Bits/pixel: 32
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 22964 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal magnification: 20000
Sample stageSpecimen holder model: JEOL 3200FSC CRYOHOLDER

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Image processing

CTF correctionDetails: CTF fit for each frame, corrected for each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: OTHER / Software - Name: MPSA, EMAN2 / Number images used: 1385

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