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Open data
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Basic information
Entry | Database: PDB / ID: 6iic | |||||||||
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Title | CryoEM structure of Mud Crab Dicistrovirus | |||||||||
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![]() | VIRUS / Dicistrovirus | |||||||||
Function / homology | Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Structural polyprotein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Zhang, Q. / Gao, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-electron Microscopy 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. In this study, 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. In this study, 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 a 3.5-Å resolution reveals three major capsid proteins (VP1 to VP3) organized into a pseudo-T=3 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 a 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. Here 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 three-dimensional (3D) structure of the mud crab tombus-like virus (MCTV) and mud crab dicistrovirus (MCDV) determined in this study 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. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 142.9 KB | Display | ![]() |
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PDB format | ![]() | 106 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 9673MC ![]() 9754C ![]() 9755C ![]() 9756C ![]() 6izlC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
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Components
#1: Protein | Mass: 20691.158 Da / Num. of mol.: 1 / Fragment: UNP residues 760-950 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 28074.658 Da / Num. of mol.: 1 / Fragment: UNP residues 1-253 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 48249.680 Da / Num. of mol.: 1 / Fragment: UNP residues 312-759 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: Protein | Mass: 5792.425 Da / Num. of mol.: 1 / Fragment: UNP residues 254-311 / Source method: isolated from a natural source / Source: (natural) ![]() |
Sequence details | Authors state that these conflicts are due to error in database. |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Mud crab dicistrovirus / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Scylla paramamosain |
Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 80 K |
Image recording | Average exposure time: 1 sec. / Electron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Num. of grids imaged: 3 |
Image scans | Sampling size: 15 µm / Width: 4096 / Height: 4096 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31801 / Algorithm: BACK PROJECTION / Num. of class averages: 2 / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |