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- PDB-5ms1: Cowpea mosaic virus top component (CPMV-T) - naturally occurring ... -

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Basic information

Entry
Database: PDB / ID: 5ms1
TitleCowpea mosaic virus top component (CPMV-T) - naturally occurring empty particles
Components
  • Large subunit of Cowpea music virus
  • Small subunit of cowpea mosaic virus
KeywordsVIRUS / CPMV-T / plant virus / picornavirales
Function / homology
Function and homology information


transport of virus in host, cell to cell / host cell plasmodesma / T=3 icosahedral viral capsid / symbiont-mediated suppression of host innate immune response / : / host cell nucleus / GTP binding / structural molecule activity / DNA binding / RNA binding
Similarity search - Function
Large coat protein / RNA2 polyprotein / Large coat protein / Small coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesCowpea mosaic virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsHesketh, E.L. / Meshcheriakova, Y. / Thompson, R.F. / Lomonossoff, G.P. / Ranson, N.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L020955/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J004596/1 United Kingdom
CitationJournal: Sci Rep / Year: 2017
Title: The structures of a naturally empty cowpea mosaic virus particle and its genome-containing counterpart by cryo-electron microscopy.
Authors: Emma L Hesketh / Yulia Meshcheriakova / Rebecca F Thompson / George P Lomonossoff / Neil A Ranson /
Abstract: Cowpea mosaic virus (CPMV) is a picorna-like plant virus. As well as an intrinsic interest in CPMV as a plant pathogen, CPMV is of major interest in biotechnology applications such as nanotechnology. ...Cowpea mosaic virus (CPMV) is a picorna-like plant virus. As well as an intrinsic interest in CPMV as a plant pathogen, CPMV is of major interest in biotechnology applications such as nanotechnology. Here, we report high resolution cryo electron microscopy (cryo-EM) maps of wild type CPMV containing RNA-2, and of naturally-formed empty CPMV capsids. The resolution of these structures is sufficient to visualise large amino acids. We have refined an atomic model for each map and identified an essential amino acid involved in genome encapsidation. This work has furthered our knowledge of Picornavirales genome encapsidation and will assist further work in the development of CPMV as a biotechnological tool.
History
DepositionDec 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Experimental preparation / Category: em_sample_support / em_software
Item: _em_sample_support.grid_type / _em_software.name / _em_software.version
Revision 1.2Oct 2, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Small subunit of cowpea mosaic virus
B: Large subunit of Cowpea music virus


Theoretical massNumber of molelcules
Total (without water)64,6572
Polymers64,6572
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-31 kcal/mol
Surface area24760 Å2
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Small subunit of cowpea mosaic virus / Genome polyprotein M / P2


Mass: 23798.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cowpea mosaic virus / Production host: Nicotiana benthamiana (plant) / References: UniProt: P03599
#2: Protein Large subunit of Cowpea music virus / Genome polyprotein M / P2


Mass: 40858.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cowpea mosaic virus / Production host: Nicotiana benthamiana (plant) / References: UniProt: P03599

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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: Cowpea mosaic virus / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Cowpea mosaic virus
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Vigna unguiculata
Buffer solutionpH: 7.8
SpecimenConc.: 1.92 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 10000 nm / Nominal defocus min: 350 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 42 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1323
Image scansMovie frames/image: 7

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Processing

EM software
IDNameVersionCategory
1RELION1.3particle selection
2EPUimage acquisition
4CTFFIND3CTF correction
7UCSF Chimeramodel fitting
9RELION1.3initial Euler assignment
10RELION1.3final Euler assignment
11RELION1.3classification
12RELION1.33D reconstruction
13Rosettamodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5594
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4696 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT

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