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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 / CRPV capsid protein like / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Structural polyprotein
Function and homology information
Biological speciesMud crab virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhang, Q. / Gao, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570736 China
National Natural Science Foundation of China31672677 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
DepositionOct 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 3, 2019Group: Data collection / Database references / Source and taxonomy
Category: citation / em_entity_assembly_naturalsource
Item: _citation.journal_volume / _citation.title / _em_entity_assembly_naturalsource.organism
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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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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  • Superimposition on EM map
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Structure viewerMolecule:
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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
Polymers102,8084
Non-polymers00
Water00
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
Polymers6,168,475240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
Polymers514,04020
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
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
Polymers616,84824
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein VP1 of Mud crab dicistrovirus


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


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


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


Mass: 5792.425 Da / Num. of mol.: 1 / Fragment: UNP residues 254-311 / Source method: isolated from a natural source / 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 / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mud crab dicistrovirus / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Mud crab virus
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / 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 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 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 holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 80 K
Image recordingAverage 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 scansSampling size: 15 µm / 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 (icosahedral)
3D reconstructionResolution: 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 buildingProtocol: RIGID BODY FIT / Space: REAL

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