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- EMDB-9673: CryoEM structure of Mud Crab Dicistrovirus -

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Basic information

Entry
Database: EMDB / ID: EMD-9673
TitleCryoEM structure of Mud Crab Dicistrovirus
Map data
SampleMud crab dicistrovirus != Mud crab virus

Mud crab dicistrovirus

  • Virus: Mud crab virus
    • Protein or peptide: VP1 of Mud crab dicistrovirus
    • Protein or peptide: VP2 of Mud crab dicistrovirus
    • Protein or peptide: VP3 of Mud crab dicistrovirus
    • Protein or peptide: VP4 of Mud crab dicistrovirus
KeywordsDicistrovirus / VIRUS
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
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 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, 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-6iic
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6iic
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9673.png

Downloads & links

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Map

FileDownload / File: emd_9673.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.933 Å
Density
Contour LevelBy AUTHOR: 3.5 / Movie #1: 3.5
Minimum - Maximum-13.330893 - 13.997154
Average (Standard dev.)-0.010499333 (±0.8961877)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 477.696 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9330.9330.933
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z477.696477.696477.696
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-13.33113.997-0.010

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Supplemental data

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Sample components

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Entire : Mud crab dicistrovirus

EntireName: Mud crab dicistrovirus
Components
  • Virus: Mud crab virus
    • Protein or peptide: VP1 of Mud crab dicistrovirus
    • Protein or peptide: VP2 of Mud crab dicistrovirus
    • Protein or peptide: VP3 of Mud crab dicistrovirus
    • Protein or peptide: VP4 of Mud crab dicistrovirus

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Supramolecule #1: Mud crab virus

SupramoleculeName: Mud crab virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 932662 / Sci species name: Mud crab virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Scylla paramamosain (green mud crab)

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Macromolecule #1: VP1 of Mud crab dicistrovirus

MacromoleculeName: VP1 of Mud crab dicistrovirus / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mud crab virus
Molecular weightTheoretical: 20.691158 KDa
SequenceString:
GGGMDYAKSD SSSLVTTMGE QFRSLRMLTR RSSPTDVLTG TSVTLPGITI GTDSSLRQSV LNIISYMYRF TKGSISYKII PKIKGDLYI TTSSADNIEL NSNAYSFDVN RALHYQNTAL NPVVQVSLPY YCPSENLVID STSFPNLSNL VLTNLERSSN T YTVLVSAG DDHTFSQLAG CPAFTIGPSR SAA

UniProtKB: Structural polyprotein

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Macromolecule #2: VP2 of Mud crab dicistrovirus

MacromoleculeName: VP2 of Mud crab dicistrovirus / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mud crab virus
Molecular weightTheoretical: 28.074658 KDa
SequenceString: MDSSVTNTGG LMPSATISNS EGATMLLNDI PDPTQNVFLS RNVTDNLFEV QDQNLIESLS REVLLGTGTW QSGQAEISTT LTEQQLITN YEQPSIRQIS LPDDIVKGSS FIASKLANIA YMRCDYELYL RVQGSPFLQG LLLLWNKMNA DQTSKIRSSI T EHLRSITS ...String:
MDSSVTNTGG LMPSATISNS EGATMLLNDI PDPTQNVFLS RNVTDNLFEV QDQNLIESLS REVLLGTGTW QSGQAEISTT LTEQQLITN YEQPSIRQIS LPDDIVKGSS FIASKLANIA YMRCDYELYL RVQGSPFLQG LLLLWNKMNA DQTSKIRSSI T EHLRSITS FPGVTLNMQS DSRSVKLVIP YTSEFQVFNP RNENKLNSVR LSILSALRGP STSEKATYSI MGRMTNIKLY GH APSIVSL SYPQTE

UniProtKB: Structural polyprotein

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Macromolecule #3: VP3 of Mud crab dicistrovirus

MacromoleculeName: VP3 of Mud crab dicistrovirus / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mud crab virus
Molecular weightTheoretical: 48.24968 KDa
SequenceString: SKDRDLSKVS PYENIPAKGF THGVGFDYGV PLSLFPDNAI DPTIANPESI DEMSIQYLAS RPYMLDRYTI KGGNTPSPSG TVVADIPIS PVNYSLYGSI IRDYRTIFGA PVSLAVAMAS WWRAKIHLNL QFAKTQYHQC RLLVQYLPYG SDVQSLENVL S QIIDISHV ...String:
SKDRDLSKVS PYENIPAKGF THGVGFDYGV PLSLFPDNAI DPTIANPESI DEMSIQYLAS RPYMLDRYTI KGGNTPSPSG TVVADIPIS PVNYSLYGSI IRDYRTIFGA PVSLAVAMAS WWRAKIHLNL QFAKTQYHQC RLLVQYLPYG SDVQSLENVL S QIIDISHV DESGIDLCFP SIFTNKWMRS YDPATEGYTA GCAPGRILIS VLNPLISAST VNDDIVMMPW LTWENLELAE PG SLAKAAI GFDYPADAVD EKWTSRELPV TGSSFNLFRD TTIVLGASTN ISNLVLTNDD TGGDYQIVST TPTGSYVSAV TCP QGTYTI THDGVGATII SNFPILGAGE GPSFQISALR HGDKVTITED PTKINVSGVS FLTGTNSWKA SLKDSSGTLL GRLE YDGTS FSSDSPASLI PGKYNVELDP ADNSAVVTIV ANNSFGTASL DTH

UniProtKB: Structural polyprotein

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Macromolecule #4: VP4 of Mud crab dicistrovirus

MacromoleculeName: VP4 of Mud crab dicistrovirus / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mud crab virus
Molecular weightTheoretical: 5.792425 KDa
SequenceString:
GGDDATASQR GIVTQVADTV SSISNVVDGL GVPLLSSISK PIGWVSNVVS NVASIFGF

UniProtKB: Structural polyprotein

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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 - 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 80.0 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 / Number grids imaged: 3 / Average exposure time: 1.0 sec. / Average electron dose: 20.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationNumber classes: 4
Final angle assignmentType: ANGULAR RECONSTITUTION
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 / Number images used: 31801
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6iic:
CryoEM structure of Mud Crab Dicistrovirus

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