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

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Basic information

Entry
Database: PDB / ID: 9qvh
TitleTurnip Crinkle Virus: virus-like particles (TCV-P38)
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: 3.47 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. 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.
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: 3.37 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: 5315
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: 97845
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2699 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 119 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: cross-correlation coefficient
Atomic model buildingPDB-ID: 9QVF

9qvf


Accession code: 9QVF / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00278120
ELECTRON MICROSCOPYf_angle_d0.43106092
ELECTRON MICROSCOPYf_dihedral_angle_d3.39110802
ELECTRON MICROSCOPYf_chiral_restr0.04111808
ELECTRON MICROSCOPYf_plane_restr0.00413848

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