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- EMDB-9756: Empty particle structure of heated mud crab dicistrovirus -

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Basic information

Entry
Database: EMDB / ID: 9756
TitleEmpty particle structure of heated mud crab dicistrovirus
Map data
SampleMud crab dicistrovirus:
virus
SourceMud crab dicistrovirus
Methodsingle particle reconstruction / cryo EM / 7.4 Å resolution
AuthorsZhang Q / Gao Y
CitationJournal: J. Virol. / Year: 2019
Title: Cryo-EM structures of novel viruses from mud crab with multiple infections.
Authors: Yuanzhu Gao / Shanshan Liu / Jiamiao Huang / Qianqian Wang / Kunpeng Li / Jian He / Jianguo He / Shaoping Weng / Qinfen Zhang
Abstract: Viruses associated with sleeping disease (SD) in crabs cause great economic losses to aquaculture, and no effective measures are available for their prevention. Herein, to help develop novel ...Viruses associated with sleeping disease (SD) in crabs cause great economic losses to aquaculture, and no effective measures are available for their prevention. Herein, to help develop novel antiviral strategies, single-particle cryo-electron microscopy was applied to investigate viruses associated with SD. The results not only revealed the structure of mud crab dicistrovirus (MCDV), but also identified a novel mud crab tombus-like virus (MCTV) not previously detected using molecular biology methods. The structure of MCDV at 3.5 Å resolution reveals three major capsid proteins (VP1-3) organized into a pseudo-T3 icosahedral capsid, and affirms the existence of VP4. Unusually, MCDV VP3 contains a long C-terminal region and forms a novel protrusion that has not been observed in other dicistrovirus. Our results also reveal that MCDV can release its genome via conformation changes of the protrusions when viral mixtures are heated. The structure of MCTV at 3.3 Å resolution reveals a T=3 icosahedral capsid with common features of both tombusviruses and nodaviruses. Furthermore, MCTV has a novel hydrophobic tunnel beneath the 5-fold vertex and 30 dimeric protrusions composed of the P-domains of the capsid protein at the 2-fold axes that are exposed on the virion surface. The structural features of MCTV are consistent with a novel type of virus.Pathogen identification is vital for unknown infectious outbreaks, especially for dual or multiple infections. Sleeping disease (SD) in crabs causes great economic losses to aquaculture worldwide. Herein, we report the discovery and identification of a novel virus in mud crabs with multiple infections that was not previously detected by molecular, immune, or traditional electron microscopy (EM) methods. High resolution structures of pathogenic viruses are essential for a molecular understanding and developing new disease prevention methods. The 3D structure of the mud crab tombus-like virus (MCTV) and mud crab dicistrovirus (MCDV) determined herein could assist the development of antiviral inhibitors. The identification of a novel virus in multiple infections previously missed using other methods demonstrates the usefulness of this strategy for investigating multiple infectious outbreaks, even in humans and other animals.
DateDeposition: Dec 19, 2018 / Header (metadata) release: Jan 16, 2019 / Map release: Jan 16, 2019 / Last update: Feb 6, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9756.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
1.09 Å/pix.
= 436. Å
400 pix
1.09 Å/pix.
= 436. Å
400 pix
1.09 Å/pix.
= 436. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density
Contour Level:3.0 (by author), 3 (movie #1):
Minimum - Maximum-5.7333813 - 9.289307000000001
Average (Standard dev.)0.031776555 (0.9529075)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin-200.0-200.0-200.0
Limit199.0199.0199.0
Spacing400400400
CellA=B=C: 436.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z436.000436.000436.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-6-10-25
NX/NY/NZ564636
MAP C/R/S123
start NC/NR/NS-200-200-200
NC/NR/NS400400400
D min/max/mean-5.7339.2890.032

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Supplemental data

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Sample components

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Entire Mud crab dicistrovirus

EntireName: Mud crab dicistrovirus / Number of components: 1

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Component #1: virus, Mud crab dicistrovirus

VirusName: Mud crab dicistrovirus / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: SPECIES
SpeciesSpecies: Mud crab dicistrovirus

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.2
VitrificationCryogen name: ETHANE / Temperature: 293 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 100000.0 X (nominal) / Cs: 1.2 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: K ( 95.0 - 100.0 K)
CameraDetector: FEI EAGLE (4k x 4k)

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Image acquisition

Image acquisitionSampling size: 15 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 3914
3D reconstructionSoftware: RELION / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF

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