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

Basic information

• Entry: Database: EMDB / ID: EMD-9756
• Title: Empty particle structure of heated mud crab dicistrovirus

Sample

• Virus: Mud crab dicistrovirus

• Biological species: Mud crab dicistrovirus
• Method: single particle reconstruction / cryo EM / Resolution: 7.4 Å
• Authors: Zhang Q / Gao Y
• Citation: Journal: J Virol / Year: 2019; 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 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

Deposition	Dec 19, 2018	-
Header (metadata) release	Jan 16, 2019	-
Map release	Jan 16, 2019	-
Update	May 1, 2019	-
Current status	May 1, 2019	Processing site: PDBj / Status: Released

Map

• File: Download / File: emd_9756.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.09 Å

Density

Contour Level	By AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum	-5.7333813 - 9.289307000000001
Average (Standard dev.)	0.031776555 (±0.9529075)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin -200 -200 -200 Dimensions 400 400 400 Spacing 400 400 400
Cell	A=B=C: 436.0 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.09	1.09	1.09
M x/y/z	400	400	400
origin x/y/z	0.000	0.000	0.000
length x/y/z	436.000	436.000	436.000
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	-200	-200	-200
NC/NR/NS	400	400	400
D min/max/mean	-5.733	9.289	0.032

Supplemental data

Sample components

Entire : Mud crab dicistrovirus

• Entire: Name: Mud crab dicistrovirus

Components

• Virus: Mud crab dicistrovirus

Supramolecule #1: Mud crab dicistrovirus

• Supramolecule: Name: Mud crab dicistrovirus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 932662 / Sci species name: Mud crab dicistrovirus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.2
• Grid: Model: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K

Electron microscopy

• Microscope: FEI TECNAI F20
• Electron beam: Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.2 mm / Nominal magnification: 100000
• Sample stage: Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER; Cooling holder cryogen: NITROGEN
• Temperature: Min: 95.0 K / Max: 100.0 K
• Image recording: Film or detector model: FEI EAGLE (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 15.0 µm / Average electron dose: 20.0 e/Ų
• Experimental equipment: Model: Tecnai F20 / Image courtesy: FEI Company

Image processing

• CTF correction: Software - Name: Gctf (ver. 1.06)
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD
• Final reconstruction: Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 3914