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- EMDB-53398: Turnip Crinkle Virus: virus-like particles (TCV-P38) -

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Basic information

Entry
Database: EMDB / ID: EMD-53398
TitleTurnip Crinkle Virus: virus-like particles (TCV-P38)
Map dataSharpened map at 3.47 A resolution used for model building and refinement
Sample
  • Virus: Turnip crinkle virus
    • Protein or peptide: Capsid protein
KeywordsssRNA plant virus / icosahedral / RNA packaging / VIRUS LIKE PARTICLE
Function / homologyPlant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / T=3 icosahedral viral capsid / Viral coat protein subunit / symbiont-mediated suppression of host innate immune response / structural molecule activity / RNA binding / Capsid protein
Function and homology information
Biological speciesTurnip crinkle virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsSaunders K / Shah S / Peyret H / Meshcheriakova Y / Richardson J / Eltschkner S / Lawson DM / Lomonossoff G
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X01097X/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/Y005732/1 United Kingdom
CitationJournal: J Mol Biol / Year: 2025
Title: The Specificity of RNA Packaging in Isometric RNA Plant Viruses is Principally Determined by Replication.
Authors: Keith Saunders / Sachin N Shah / Hadrien Peyret / Yulia Meshcheriakova / Jake Richardson / Sandra Eltschkner / David M Lawson / George P Lomonossoff /
Abstract: A potato virus X (PVX)-based transient expression system (pEff) that produces replicating RNA has been used to examine the specificity of RNA packaging in the isometric viruses, turnip crinkle virus ...A potato virus X (PVX)-based transient expression system (pEff) that produces replicating RNA has been used to examine the specificity of RNA packaging in the isometric viruses, turnip crinkle virus (TCV) and satellite tobacco necrosis virus-1 (STNV-1). Expression of the coat proteins from the subgenomic RNA derived from the replicating PVX genome results in the efficient production of virus-like particles (VLPs), indistinguishable in structure from native virus particles, and encapsidation of both the subgenomic RNA and truncated versions of the replicating genomic RNA. Non-specific encapsidation of host RNA (which is not replicating) could not be detected in this system, implying that replication is the major determinant of packaging in isometric as well as filamentous positive-strand RNA plant viruses. We further utilised the system to investigate the role of putative packaging signals previously identified within the coat protein open reading frames of both TCV and STNV-1. The results show that eliminating the hairpin structures previously identified as packaging signals has no detectable effect on the specificity of RNA packaging. Replacement of the 213 nucleotide sequence within the TCV coat protein coding region, believed to be important for genomic packaging, with an equivalent sequence codon-optimised for Plasmodium falciparum resulted in less efficient capsid formation and RNA packaging, but did not alter packaging specificity; addition of copies of the wild-type sequence did not complement the defects. We propose that replication is the major determinant of genome packaging specificity in plant RNA viruses, while packaging signals may play a role in packaging efficiency.
History
DepositionApr 11, 2025-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53398.png

Downloads & links

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Map

FileDownload / File: emd_53398.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map at 3.47 A resolution used for model building and refinement
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.26 Å/pix.
x 560 pix.
= 704.984 Å		1.26 Å/pix.
x 560 pix.
= 704.984 Å		1.26 Å/pix.
x 560 pix.
= 704.984 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2589 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.91635185 - 1.786761
Average (Standard dev.)-0.0043528886 (±0.066343084)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 704.984 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53398_msk_1.map
Projections & Slices
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Additional map: Unsharpened map

Fileemd_53398_additional_1.map
AnnotationUnsharpened map
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Half map: Half map 2

Fileemd_53398_half_map_1.map
AnnotationHalf map 2
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Half map: Half map 1

Fileemd_53398_half_map_2.map
AnnotationHalf map 1
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Sample components

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Entire : Turnip crinkle virus

EntireName: Turnip crinkle virus
Components
  • Virus: Turnip crinkle virus
    • Protein or peptide: Capsid protein

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Supramolecule #1: Turnip crinkle virus

SupramoleculeName: Turnip crinkle virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: In the manuscript, this sample is designated TCV-P38. The complete P38 coat protein gene was inserted into the pEff vector. Expression was initiated by infiltrating leaves of Nicotiana ...Details: In the manuscript, this sample is designated TCV-P38. The complete P38 coat protein gene was inserted into the pEff vector. Expression was initiated by infiltrating leaves of Nicotiana benthamiana with suspensions of Agrobacterium tumefaciens strain LBA4404 harbouring this vector.
NCBI-ID: 11988 / Sci species name: Turnip crinkle virus / Sci species strain: M / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Brassica rapa subsp. rapa (turnip)
Molecular weightTheoretical: 6.86 MDa
Virus shellShell ID: 1 / Name: capsid / Diameter: 340.0 Å / T number (triangulation number): 3

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Turnip crinkle virus / Strain: M
Molecular weightTheoretical: 38.170941 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MENDPRVRKF ASDGAQWAIK WQKKGWSTLT SRQKQTARAA MGIKLSPVAQ PVQKVTRLSA PVALAYREVS TQPRVSTARD GITRSGSEL ITTLKKNTDT EPKYTTAVLN PSEPGTFNQL IKEAAQYEKY RFTSLRFRYS PMSPSTTGGK VALAFDRDAA K PPPNDLAS ...String:
MENDPRVRKF ASDGAQWAIK WQKKGWSTLT SRQKQTARAA MGIKLSPVAQ PVQKVTRLSA PVALAYREVS TQPRVSTARD GITRSGSEL ITTLKKNTDT EPKYTTAVLN PSEPGTFNQL IKEAAQYEKY RFTSLRFRYS PMSPSTTGGK VALAFDRDAA K PPPNDLAS LYNIEGCVSS VPWTGFILTV PTDSTDRFVA DGISDPKLVD FGKLIMATYG QGANDAAQLG EVRVEYTVQL KN RTGSTSD AQIGDFAGVK DGPRLVSWSK TKGTAGWEHD CHFLGTGNFS LTLFYEKAPV SGLENADASD FSVLGEAAAG SVQ WAGVKV AERGQGVKMV TTEEQPKGKW QALRI

UniProtKB: Capsid protein

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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

Concentration4.0 mg/mL
BufferpH: 7.4 / Details: 1 mM MgSO4 1mM NaPO4 and pH7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
Details: glow discharged for 60 seconds at 8 mA using an ACE 200 (Leica Microsystems)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS TALOS F200C
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 5315 / Average exposure time: 3.37 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 150000
Sample stageSpecimen holder model: GATAN ELSA 698 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 97845
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9qvf

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 2699
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9qvf


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 119 / Target criteria: cross-correlation coefficient
Output model

PDB-9qvh:
Turnip Crinkle Virus: virus-like particles (TCV-P38)

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