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

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Basic information

Entry
Database: EMDB / ID: EMD-9754
TitleCryo-EM structure of Mud crab tombus-like virus at 3.3 Angstroms resolution
Map data
SampleViruses != Wenzhou tombus-like virus 18

Viruses

  • Virus: Wenzhou tombus-like virus 18
    • Protein or peptide: mud crab tombus-like virus
Keywordsvirus / capsid
Function / homologyIcosahedral viral capsid protein, S domain / Viral coat protein (S domain) / Viral coat protein subunit / viral capsid / structural molecule activity / Capsid protein
Function and homology information
Biological speciesWenzhou tombus-like virus 18
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhang Q / Gao Y
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China31672677 China
National Natural Science Foundation of China31570736 China
CitationJournal: 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 ...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
DepositionDec 19, 2018-
Header (metadata) releaseJan 16, 2019-
Map releaseJan 16, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • 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 modelsPDB-6izl
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9754.png

Downloads & links

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Map

FileDownload / File: emd_9754.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 480 pix.
= 447.84 Å		0.93 Å/pix.
x 480 pix.
= 447.84 Å		0.93 Å/pix.
x 480 pix.
= 447.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.933 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5 / Movie #1: 3.5
Minimum - Maximum-7.9060407 - 14.174388
Average (Standard dev.)-0.0024322476 (±0.8975434)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 447.84003 Å
α=β=γ: 90.0 °

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
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-7.90614.174-0.002

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Supplemental data

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Sample components

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Entire : Viruses

EntireName: Viruses
Components
  • Virus: Wenzhou tombus-like virus 18
    • Protein or peptide: mud crab tombus-like virus

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Supramolecule #1: Wenzhou tombus-like virus 18

SupramoleculeName: Wenzhou tombus-like virus 18 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1923671 / Sci species name: Wenzhou tombus-like virus 18 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Scylla paramamosain (green mud crab)
Virus shellShell ID: 1 / T number (triangulation number): 3

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Macromolecule #1: mud crab tombus-like virus

MacromoleculeName: mud crab tombus-like virus / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Wenzhou tombus-like virus 18
Molecular weightTheoretical: 36.813723 KDa
SequenceString: MTGSNRRANA GRKTQPKPQR KPRAPRRPKV QNAPRIQQGG GPVPLLESNS NMRQMHNGMT RVVGSDYLGV VSVAGNPADA AAKVRKVLS VSPSSFPGTR LTQMSDLWER YVFRQFRVRY VPSVPNTLAC QVMVYQDTDP QDDPTAIKDA DALLRQATAQ T GSQQWNFN ...String:
MTGSNRRANA GRKTQPKPQR KPRAPRRPKV QNAPRIQQGG GPVPLLESNS NMRQMHNGMT RVVGSDYLGV VSVAGNPADA AAKVRKVLS VSPSSFPGTR LTQMSDLWER YVFRQFRVRY VPSVPNTLAC QVMVYQDTDP QDDPTAIKDA DALLRQATAQ T GSQQWNFN SAKVIHLAKR SDNQLYYTGP VKENPRFNQQ GVVYFIQVSQ ALDMNGKPLT ADMECGSLYV DWVIDFQTPQ VN PSAVEAR LPSAGFFTRQ ILVNDKLTFA AQASLTVALT ALSATPKVWL EGPTRVDLAT LGGPGGNLVQ IELTRAQPGD YTV KFVGCD SVTLVSSAPI A

UniProtKB: Capsid protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 90.0 K / Max: 100.0 K
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr (ver. 2014-02-10) / Number images used: 41941
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: jspr (ver. 2014-02-10)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: jspr (ver. 2014-02-10)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE / Overall B value: 174.7
Output model

PDB-6izl:
Cryo-EM structure of Mud crab tombus-like virus at 3.3 Angstroms resolution

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