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- PDB-7og6: Structure of Alternanthera Mosaic VLP by cryoEM -

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Basic information

Entry
Database: PDB / ID: 7og6
TitleStructure of Alternanthera Mosaic VLP by cryoEM
Components
  • Coat protein
  • RNA (5'-R(P*UP*UP*UP*UP*U)-3')
KeywordsVIRUS LIKE PARTICLE / Potexvirus / VLP.
Function / homologyPotexviruses and carlaviruses coat protein signature. / Potex/carlavirus coat protein / Viral coat protein / viral capsid / structural molecule activity / RNA / Coat protein
Function and homology information
Biological speciesAlternanthera mosaic virus
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsByrne, M.J. / Ranson, N.A. / Lomonossoff, G.P. / Thuenemann, E.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R00160X/1 United Kingdom
CitationJournal: Viruses / Year: 2021
Title: A Replicating Viral Vector Greatly Enhances Accumulation of Helical Virus-Like Particles in Plants.
Authors: Eva C Thuenemann / Matthew J Byrne / Hadrien Peyret / Keith Saunders / Roger Castells-Graells / Inmaculada Ferriol / Mattia Santoni / John F C Steele / Neil A Ranson / Linda Avesani / Juan ...Authors: Eva C Thuenemann / Matthew J Byrne / Hadrien Peyret / Keith Saunders / Roger Castells-Graells / Inmaculada Ferriol / Mattia Santoni / John F C Steele / Neil A Ranson / Linda Avesani / Juan Jose Lopez-Moya / George P Lomonossoff /
Abstract: The production of plant helical virus-like particles (VLPs) via plant-based expression has been problematic with previous studies suggesting that an RNA scaffold may be necessary for their efficient ...The production of plant helical virus-like particles (VLPs) via plant-based expression has been problematic with previous studies suggesting that an RNA scaffold may be necessary for their efficient production. To examine this, we compared the accumulation of VLPs from two potexviruses, papaya mosaic virus and alternanthera mosaic virus (AltMV), when the coat proteins were expressed from a replicating potato virus X- based vector (pEff) and a non-replicating vector (pEAQ-). Significantly greater quantities of VLPs could be purified when pEff was used. The pEff system was also very efficient at producing VLPs of helical viruses from different virus families. Examination of the RNA content of AltMV and tobacco mosaic virus VLPs produced from pEff revealed the presence of vector-derived RNA sequences, suggesting that the replicating RNA acts as a scaffold for VLP assembly. Cryo-EM analysis of the AltMV VLPs showed they had a structure very similar to that of authentic potexvirus particles. Thus, we conclude that vectors generating replicating forms of RNA, such as pEff, are very efficient for producing helical VLPs.
History
DepositionMay 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Coat protein
R: RNA (5'-R(P*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)23,7302
Polymers23,7302
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Coat protein


Mass: 22243.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alternanthera mosaic virus / Gene: CP / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q52Z61
#2: RNA chain RNA (5'-R(P*UP*UP*UP*UP*U)-3')


Mass: 1485.872 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alternanthera mosaic virus / Production host: Nicotiana benthamiana (plant)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Alternanthera mosaic virus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Alternanthera mosaic virus
Source (recombinant)Organism: Nicotiana benthamiana (plant)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 8 / Details: 10 mM Tris-HCl, pH 8.0
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / 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 FIELDBright-field microscopy
Image recordingElectron dose: 1.11 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM softwareName: RELION / Version: 3.1 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 41.11 ° / Axial rise/subunit: 3.959 Å / Axial symmetry: C1
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32018 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0071668
ELECTRON MICROSCOPYf_angle_d0.6552302
ELECTRON MICROSCOPYf_dihedral_angle_d21.533274
ELECTRON MICROSCOPYf_chiral_restr0.044275
ELECTRON MICROSCOPYf_plane_restr0.006285

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