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

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Entry
Database: PDB / ID: 6izl
TitleCryo-EM structure of Mud crab tombus-like virus at 3.3 Angstroms resolution
Componentsmud crab tombus-like virus
KeywordsVIRUS / virus / capsid
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
Specimen sourceWenzhou tombus-like virus 18
MethodELECTRON MICROSCOPY / single 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 Report
SummaryFull reportAbout validation report
DateDeposition: Dec 19, 2018 / Release: Jan 16, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 16, 2019Structure modelrepositoryInitial release
1.1Feb 6, 2019Structure modelData collection / Database referencescitation / citation_author_citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: mud crab tombus-like virus
B: mud crab tombus-like virus
C: mud crab tombus-like virus


Theoretical massNumber of molelcules
Total (without water)110,4413
Polyers110,4413
Non-polymers00
Water0
1
A: mud crab tombus-like virus
B: mud crab tombus-like virus
C: mud crab tombus-like virus
x 60


Theoretical massNumber of molelcules
Total (without water)6,626,470180
Polyers6,626,470180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
Buried area (Å2)7960
ΔGint (kcal/M)-11
Surface area (Å2)29980
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: mud crab tombus-like virus
B: mud crab tombus-like virus
C: mud crab tombus-like virus
x 5


  • icosahedral pentamer
  • 552 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)552,20615
Polyers552,20615
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: mud crab tombus-like virus
B: mud crab tombus-like virus
C: mud crab tombus-like virus
x 6


  • icosahedral 23 hexamer
  • 663 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)662,64718
Polyers662,64718
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

#1: Protein/peptide mud crab tombus-like virus


Mass: 36813.723 Da / Num. of mol.: 3 / Source: (natural) Wenzhou tombus-like virus 18 / References: UniProt: A0A1L3KFA2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Viruses / Type: VIRUS / Entity ID: 1 / Source: NATURAL
Source (natural)Organism: Wenzhou tombus-like virus 18
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: SPECIES / Virus type: VIRION
Natural hostOrganism: Scylla paramamosain
Virus shellTriangulation number (T number): 3
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 96000 / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 kelvins / Temperature (min): 90 kelvins
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansSampling size: 15 microns / Width: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1EMAN22.1particle selection
7Coot0.7.2.1model fitting
9jspr2014-02-10initial Euler assignment
10jspr2014-02-10final Euler assignment
11RELION2.0classification
12jspr2014-02-103D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: I
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 41941 / Algorithm: BACK PROJECTION / Number of class averages: 2 / Symmetry type: POINT
Atomic model buildingOverall b value: 174.7 / Ref protocol: BACKBONE TRACE / Ref space: REAL

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