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- EMDB-25398: CSDaV wilde-type -

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Basic information

Entry
Database: EMDB / ID: EMD-25398
TitleCSDaV wilde-type
Map dataThe mature whole capsid density map of wild type citrus sudden death-associated virus (CSDaV)
Sample
  • Virus: Citrus sudden death-associated virus
    • Protein or peptide: Citrus Sudden Death-associated Virus Capsid Protein
KeywordsCapsid / coat protein / VIRUS
Function / homology
Function and homology information


mRNA methyltransferase activity / mRNA modification / RNA processing / viral capsid / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity ...mRNA methyltransferase activity / mRNA modification / RNA processing / viral capsid / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / proteolysis / RNA binding / ATP binding
Similarity search - Function
Peptidase C21 / Tymovirus endopeptidase domain / Salyut domain / Tymovirus endopeptidase / Salyut domain / Peptidase family C21 domain profile. / Tymovirus coat protein / Tymovirus coat protein / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain ...Peptidase C21 / Tymovirus endopeptidase domain / Salyut domain / Tymovirus endopeptidase / Salyut domain / Peptidase family C21 domain profile. / Tymovirus coat protein / Tymovirus coat protein / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Viral (Superfamily 1) RNA helicase / Viral coat protein subunit / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesCitrus sudden death-associated virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsGuo F / Matsumura EE
Funding support United States, 1 items
OrganizationGrant numberCountry
United States Department of Agriculture (USDA)2015-70016-230 United States
Citation
Journal: Biotechnol Rep (Amst) / Year: 2022
Title: Citrus sudden death-associated virus as a new expression vector for rapid production of heterologous proteins, chimeric virions, and virus-like particles.
Authors: Emilyn E Matsumura / Fei Guo / Daan Boogers / Dennis van Oevelen / Sandra T Vu / Bryce W Falk /
Abstract: The more we understand the strategies used by viruses for protein expression, the more possibilities we have to exploit viruses as expression vectors for heterologous protein production. Advances in ...The more we understand the strategies used by viruses for protein expression, the more possibilities we have to exploit viruses as expression vectors for heterologous protein production. Advances in the development of virus-based expression systems have been possible due to generation of many virus infectious clones, especially those derived from plant viruses, which have the capability for rapid and high-level transient expression of proteins in plant cells, a robust and low-cost bioreactor. In this work, we generated new replicative virus expression vectors based on a previously constructed citrus sudden death-associated virus (CSDaV) infectious cDNA clone. These vectors were generated to express the reporter green fluorescent protein (GFP) in leaves by taking advantage of the expression strategies used by CSDaV to produce its structural proteins. We show that higher amounts of GFP can be produced from a coat protein (CP)-independent CSDaV-based vector, compared to levels of GFP expressed from a widely used non-replicative vector (pEAQ series); or GFP can be produced in fusion with the major CSDaV CP (CPp21) to be incorporated into chimeric virions. However, GFP-recombinant CSDaV virions do not appear uniformly assembled, but more likely as mosaic particles. Cryo-electron microscopy analysis from this work revealed the structures of the wild-type and the GFP-recombinant CSDaV virions, but it was not able to reveal where exactly the GFP is displayed in the chimeric virions. We show though that the incorporation of GFP-CPp21 fusion protein into virions occurs solely due to its interaction with free/non-fused CPp21, independent of other viral proteins. Therefore, individual co-expression of GFP-CPp21 and CPp21 in the same plant cells leads to the production of chimeric virus-like particles (VLPs), while GFP-CPp21 fusion protein itself is not able to self-assemble into VLPs. The new CSDaV-based expression vectors may provide an alternative platform for use in molecular farming, either for production of heterologous proteins or as scaffold for heterologous protein display.
#1: Journal: To Be Published
Title: Rescue of Citrus sudden death-associated virus in Nicotiana benthamiana plants from cloned cDNA: insights into mechanisms of expression of the three capsid proteins
Authors: Matsumura EE / Coletta-Filho HD / Machado MA / Nouri S / Falk BW
History
DepositionNov 7, 2021-
Header (metadata) releaseMay 25, 2022-
Map releaseMay 25, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25398.png

Downloads & links

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Map

FileDownload / File: emd_25398.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe mature whole capsid density map of wild type citrus sudden death-associated virus (CSDaV)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 512 pix.
= 450.56 Å		0.88 Å/pix.
x 512 pix.
= 450.56 Å		0.88 Å/pix.
x 512 pix.
= 450.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0326
Minimum - Maximum-0.15361205 - 0.20636792
Average (Standard dev.)0.0003048386 (±0.009026195)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 450.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Citrus sudden death-associated virus

EntireName: Citrus sudden death-associated virus
Components
  • Virus: Citrus sudden death-associated virus
    • Protein or peptide: Citrus Sudden Death-associated Virus Capsid Protein

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Supramolecule #1: Citrus sudden death-associated virus

SupramoleculeName: Citrus sudden death-associated virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 312008 / Sci species name: Citrus sudden death-associated virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Citrus (plant)

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Macromolecule #1: Citrus Sudden Death-associated Virus Capsid Protein

MacromoleculeName: Citrus Sudden Death-associated Virus Capsid Protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Citrus sudden death-associated virus
Molecular weightTheoretical: 20.75441 KDa
Recombinant expressionOrganism: Agrobacterium tumefaciens (bacteria)
SequenceString: MASDAQAGPA PSRDDRVDRQ PRLPAAPRVA EVGLNAPSVD YPFQWVVASY DGSEAKNLSD DLSGSATLTK VMANYRHAEL TSVELEVCP LAAAFSKPIS VSAVWTIASI SPASASETSY YGGRLFTVGG PVLMSSTTHL PADLTRLNPV LKGPVKYTDC P RFSYSVYS ...String:
MASDAQAGPA PSRDDRVDRQ PRLPAAPRVA EVGLNAPSVD YPFQWVVASY DGSEAKNLSD DLSGSATLTK VMANYRHAEL TSVELEVCP LAAAFSKPIS VSAVWTIASI SPASASETSY YGGRLFTVGG PVLMSSTTHL PADLTRLNPV LKGPVKYTDC P RFSYSVYS NGGTKGTNLC TIILRGVVRL SGPSGNLLA

UniProtKB: 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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0002 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK III
Details: blot for 8 seconds before plunging with -2mm off set.

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Electron microscopy

MicroscopeTFS GLACIOS
TemperatureMin: 90.0 K / Max: 90.0 K
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 2481 / Average exposure time: 3.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 56818 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Details: Relion is used for finial reconstruction / Number images used: 175869
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7sqz:
CSDaV wild-type

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