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- EMDB-53396: Turnip Crinkle Virus: virus-like particles (TCV-P38+1) -

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Basic information

Entry
Database: EMDB / ID: EMD-53396
TitleTurnip Crinkle Virus: virus-like particles (TCV-P38+1)
Map dataSharpened map at 3.13 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: 3.13 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: To Be Published
Title: The specificity of RNA packaging in isometric RNA plant viruses is principally determined by replication
Authors: Saunders K / Shah S / Peyret H / Meshcheriakova Y / Richardson J / Eltschkner S / Lawson DM / Lomonossoff G
History
DepositionApr 11, 2025-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53396.png

Downloads & links

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Map

FileDownload / File: emd_53396.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map at 3.13 A resolution used for model building and refinement
Projections & slices

Image control

Size
Brightness
Contrast
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

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2589 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.52609664 - 0.98105115
Average (Standard dev.)0.0053576 (±0.03289177)
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_53396_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_53396_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Histogram

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Half map: Half map 1

Fileemd_53396_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_53396_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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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+1. The complete P38 coat protein gene was inserted into the pEff vector together with an additional duplicated portion of P38 (hence +1). ...Details: In the manuscript, this sample is designated TCV-P38+1. The complete P38 coat protein gene was inserted into the pEff vector together with an additional duplicated portion of P38 (hence +1). 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 / Pretreatment - Time: 60 sec.
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: 6269 / Average exposure time: 3.49 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: 92873
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3zx8

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 48900
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 classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.5.3)
Details: 3 ab initio classes fed directly into heterogeneous refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3zx8


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 65.3 / Target criteria: cross-correlation coefficient
Output model

PDB-9qvf:
Turnip Crinkle Virus: virus-like particles (TCV-P38+1)

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