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- EMDB-53397: Turnip Crinkle Virus: virions (TCV-M) -

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Basic information

Entry
Database: EMDB / ID: EMD-53397
TitleTurnip Crinkle Virus: virions (TCV-M)
Map dataSharpened map at 3.43 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: 3.43 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_53397.png

Downloads & links

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Map

FileDownload / File: emd_53397.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map at 3.43 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

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2589 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.37311304 - 0.76814973
Average (Standard dev.)0.0014260543 (±0.02703926)
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_53397_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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Additional map: Unsharpened map

Fileemd_53397_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_53397_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_53397_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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-M. The complete P38 coat protein gene was inserted into the pBin61 vector. Expression was initiated by infiltrating leaves of Nicotiana ...Details: In the manuscript, this sample is designated TCV-M. The complete P38 coat protein gene was inserted into the pBin61 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: VIRION / 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 R2/2 / 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: 2384 / Average exposure time: 3.46 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: 22567
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: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 9981
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:

9qvf


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 83 / Target criteria: cross-correlation coefficient
Output model

PDB-9qvg:
Turnip Crinkle Virus: virions (TCV-M)

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