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- PDB-6iic: CryoEM structure of Mud Crab Dicistrovirus -

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Basic information

Entry
Database: PDB / ID: 6iic
TitleCryoEM structure of Mud Crab Dicistrovirus
Components
  • VP1 of Mud crab dicistrovirus
  • VP2 of Mud crab dicistrovirus
  • VP3 of Mud crab dicistrovirus
  • VP4 of Mud crab dicistrovirus
KeywordsVIRUS / Dicistrovirus
Function / homologyDicistrovirus, capsid-polyprotein, C-terminal / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / CRPV capsid protein like / Structural polyprotein
Function and homology information
Specimen sourceMud crab virus
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: Oct 4, 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

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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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
  • EMDB-9673
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  • Superimposition on EM map
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP1 of Mud crab dicistrovirus
B: VP2 of Mud crab dicistrovirus
C: VP3 of Mud crab dicistrovirus
D: VP4 of Mud crab dicistrovirus


Theoretical massNumber of molelcules
Total (without water)102,8084
Polyers102,8084
Non-polymers00
Water0
1
A: VP1 of Mud crab dicistrovirus
B: VP2 of Mud crab dicistrovirus
C: VP3 of Mud crab dicistrovirus
D: VP4 of Mud crab dicistrovirus
x 60


Theoretical massNumber of molelcules
Total (without water)6,168,475240
Polyers6,168,475240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: VP1 of Mud crab dicistrovirus
B: VP2 of Mud crab dicistrovirus
C: VP3 of Mud crab dicistrovirus
D: VP4 of Mud crab dicistrovirus
x 5


  • icosahedral pentamer
  • 514 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)514,04020
Polyers514,04020
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: VP1 of Mud crab dicistrovirus
B: VP2 of Mud crab dicistrovirus
C: VP3 of Mud crab dicistrovirus
D: VP4 of Mud crab dicistrovirus
x 6


  • icosahedral 23 hexamer
  • 617 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)616,84824
Polyers616,84824
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 VP1 of Mud crab dicistrovirus


Mass: 20691.158 Da / Num. of mol.: 1 / Fragment: UNP residues 760-950 / Source: (natural) Mud crab virus / References: UniProt: E5G7H9
#2: Protein/peptide VP2 of Mud crab dicistrovirus


Mass: 28074.658 Da / Num. of mol.: 1 / Fragment: UNP residues 1-253 / Source: (natural) Mud crab virus / References: UniProt: E5G7H9
#3: Protein/peptide VP3 of Mud crab dicistrovirus


Mass: 48249.680 Da / Num. of mol.: 1 / Fragment: UNP residues 312-759 / Source: (natural) Mud crab virus / References: UniProt: E5G7H9
#4: Protein/peptide VP4 of Mud crab dicistrovirus


Mass: 5792.425 Da / Num. of mol.: 1 / Fragment: UNP residues 254-311 / Source: (natural) Mud crab virus / References: UniProt: E5G7H9
Sequence detailsAuthors state that these conflicts are due to error in database.

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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: Mud crab dicistrovirus / Type: VIRUS / Entity ID: 1, 2, 3, 4 / Source: NATURAL
Source (natural)Organism: Mud crab dicistrovirus
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: SPECIES / Virus type: VIRION
Natural hostOrganism: Scylla paramamosain
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 / 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 holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 kelvins / Temperature (min): 80 kelvins
Image recordingAverage exposure time: 1 sec. / Electron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number of grids imaged: 3
Image scansSampling size: 15 microns / Width: 4096 / Height: 4096

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Processing

EM software
IDNameCategory
7Cootmodel fitting
9PHENIXmodel refinement
13jspr3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: I
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 31801 / Algorithm: BACK PROJECTION / Number of class averages: 2 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL

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