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- EMDB-9754: Cryo-EM structure of Mud crab tombus-like virus at 3.3 Angstroms ... -

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Database: EMDB / ID: 9754
TitleCryo-EM structure of Mud crab tombus-like virus at 3.3 Angstroms resolution
Map data
virus / mud crab tombus-like virus
Function / homologyIcosahedral viral capsid protein, S domain / Viral coat protein subunit / Viral coat protein (S domain) / viral capsid / structural molecule activity / Uncharacterized protein
Function and homology information
SourceWenzhou tombus-like virus 18
Methodsingle particle reconstruction / cryo EM / 3.3 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.
Validation ReportPDB-ID: 6izl

SummaryFull reportAbout validation report
DateDeposition: Dec 19, 2018 / Header (metadata) release: Jan 16, 2019 / Map release: Jan 16, 2019 / Last update: Feb 6, 2019

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6izl
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6izl
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
Supplemental images

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Fileemd_9754.map.gz (map file in CCP4 format, 442369 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
480 pix
0.93 Å/pix.
= 447.84 Å
480 pix
0.93 Å/pix.
= 447.84 Å
480 pix
0.93 Å/pix.
= 447.84 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.933 Å
Contour Level:3.5 (by author), 3.5 (movie #1):
Minimum - Maximum-7.9060407 - 14.174388
Average (Standard dev.)-0.0024322476 (0.8975434)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 447.84003 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9330.9330.933
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z447.840447.840447.840
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-7.90614.174-0.002

Supplemental data

Sample components

Entire Viruses

EntireName: Viruses / Number of components: 2

Component #1: virus, Wenzhou tombus-like virus 18

VirusName: Wenzhou tombus-like virus 18 / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
SpeciesSpecies: Wenzhou tombus-like virus 18
Source (natural)Host Species: Scylla paramamosain (green mud crab)

Component #2: protein, mud crab tombus-like virus

ProteinName: mud crab tombus-like virus / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 36.813723 kDa
SourceSpecies: Wenzhou tombus-like virus 18

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 100 %

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 96000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 90.0 - 100.0 K)
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

Image acquisition

Image acquisitionSampling size: 15 microns

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 41941
3D reconstructionAlgorithm: BACK PROJECTION / Software: jspr / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

Atomic model buiding

Modeling #1Refinement space: REAL / Overall bvalue: 174.699999999999989
Output model

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