|Entry||Database: EMDB / ID: 9754|
|Title||Cryo-EM structure of Mud crab tombus-like virus at 3.3 Angstroms resolution|
virus / mud crab tombus-like virus
|Function / homology||Icosahedral 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
|Source||Wenzhou tombus-like virus 18|
|Method||single particle reconstruction / cryo EM / 3.3 Å resolution|
|Authors||Zhang Q / Gao Y|
|Citation||Journal: 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 Report||PDB-ID: 6izl|
SummaryFull reportAbout validation report
|Date||Deposition: Dec 19, 2018 / Header (metadata) release: Jan 16, 2019 / Map release: Jan 16, 2019 / Last update: Feb 6, 2019|
|Structure viewer||EM map: |
Downloads & links
|File||emd_9754.map.gz (map file in CCP4 format, 442369 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 0.933 Å|
CCP4 map header:
|Entire||Name: Viruses / Number of components: 2|
-Component #1: virus, Wenzhou tombus-like virus 18
|Virus||Name: Wenzhou tombus-like virus 18 / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES|
|Species||Species: Wenzhou tombus-like virus 18|
|Source (natural)||Host Species: Scylla paramamosain (green mud crab)|
-Component #2: protein, mud crab tombus-like virus
|Protein||Name: mud crab tombus-like virus / Number of Copies: 3 / Recombinant expression: No|
|Mass||Theoretical: 36.813723 kDa|
|Source||Species: Wenzhou tombus-like virus 18|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||pH: 7.2|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 96000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 90.0 - 100.0 K)|
|Camera||Detector: GATAN ULTRASCAN 4000 (4k x 4k)|
|Image acquisition||Sampling size: 15 microns|
-Atomic model buiding
|Modeling #1||Refinement space: REAL / Overall bvalue: 174.699999999999989|
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