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

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Basic information

Entry
Database: PDB / ID: 9qvf
TitleTurnip Crinkle Virus: virus-like particles (TCV-P38+1)
ComponentsCapsid protein
KeywordsVIRUS LIKE PARTICLE / ssRNA plant virus / icosahedral / RNA packaging
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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsSaunders, K. / Shah, S. / Peyret, H. / Meshcheriakova, Y. / Richardson, J. / Eltschkner, S. / Lawson, D.M. / Lomonossoff, G.
Funding support United Kingdom, 2items
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, D.M. / Lomonossoff, G.
History
DepositionApr 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein


Theoretical massNumber of molelcules
Total (without water)114,5133
Polymers114,5133
Non-polymers00
Water00
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)6,870,769180
Polymers6,870,769180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Capsid protein / Coat protein / p38


Mass: 38170.941 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Turnip crinkle virus / Strain: M / Gene: ORF4 / Production host: Nicotiana benthamiana (plant) / References: UniProt: P06663
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Turnip crinkle virus / Type: VIRUS
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.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 6.86 MDa / Experimental value: NO
Source (natural)Organism: Turnip crinkle virus / Strain: M
Source (recombinant)Organism: Nicotiana benthamiana (plant)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Brassica rapa subsp. rapa
Virus shellName: capsid / Diameter: 340 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.4 / Details: 1 mM MgSO4 1mM NaPO4 and pH7.4
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: glow discharged for 60 seconds at 8 mA using an ACE 200 (Leica Microsystems)
Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: TFS TALOS F200C
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN ELSA 698 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingAverage exposure time: 3.49 sec. / Electron dose: 30 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6269
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
2EPU3.7.1.6940image acquisition
4cryoSPARC4.5.3CTF correction
7UCSF ChimeraX1.8model fitting
8Coot0.9.8.95 EL (ccp4)model fitting
10cryoSPARC4.5.3initial Euler assignment
11cryoSPARC4.5.3final Euler assignment
12cryoSPARC4.5.3classification
13cryoSPARC4.5.33D reconstruction
14PHENIX1.21.2_5419:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 92873
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48900 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 65.3 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: cross-correlation coefficient
Atomic model buildingPDB-ID: 3ZX8

3zx8


Accession code: 3ZX8 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00378120
ELECTRON MICROSCOPYf_angle_d0.436106092
ELECTRON MICROSCOPYf_dihedral_angle_d3.78810816
ELECTRON MICROSCOPYf_chiral_restr0.04111808
ELECTRON MICROSCOPYf_plane_restr0.00313848

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