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- PDB-6s44: Faba bean necrotic stunt virus (FBNSV) -

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Basic information

Entry
Database: PDB / ID: 6s44
TitleFaba bean necrotic stunt virus (FBNSV)
ComponentsCapsid proteinCapsid
KeywordsVIRUS / icosahedral T1 capsid
Function / homologyNanovirus coat protein / Nanovirus coat protein / virion component => GO:0044423 / Capsid protein
Function and homology information
Biological speciesFaba bean necrotic stunt virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsTrapani, S. / Lai Kee Him, J. / Blanc, S. / Bron, P.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-14- 15 CE02-0014 France
CitationJournal: PLoS Pathog / Year: 2023
Title: Structure-guided mutagenesis of the capsid protein indicates that a nanovirus requires assembled viral particles for systemic infection.
Authors: Stefano Trapani / Eijaz Ahmed Bhat / Michel Yvon / Joséphine Lai-Kee-Him / François Hoh / Marie-Stéphanie Vernerey / Elodie Pirolles / Mélia Bonnamy / Guy Schoehn / Jean-Louis Zeddam / ...Authors: Stefano Trapani / Eijaz Ahmed Bhat / Michel Yvon / Joséphine Lai-Kee-Him / François Hoh / Marie-Stéphanie Vernerey / Elodie Pirolles / Mélia Bonnamy / Guy Schoehn / Jean-Louis Zeddam / Stéphane Blanc / Patrick Bron /
Abstract: Nanoviruses are plant multipartite viruses with a genome composed of six to eight circular single-stranded DNA segments. The distinct genome segments are encapsidated individually in icosahedral ...Nanoviruses are plant multipartite viruses with a genome composed of six to eight circular single-stranded DNA segments. The distinct genome segments are encapsidated individually in icosahedral particles that measure ≈18 nm in diameter. Recent studies on the model species Faba bean necrotic stunt virus (FBNSV) revealed that complete sets of genomic segments rarely occur in infected plant cells and that the function encoded by a given viral segment can complement the others across neighbouring cells, presumably by translocation of the gene products through unknown molecular processes. This allows the viral genome to replicate, assemble into viral particles and infect anew, even with the distinct genome segments scattered in different cells. Here, we question the form under which the FBNSV genetic material propagates long distance within the vasculature of host plants and, in particular, whether viral particle assembly is required. Using structure-guided mutagenesis based on a 3.2 Å resolution cryogenic-electron-microscopy reconstruction of the FBNSV particles, we demonstrate that specific site-directed mutations preventing capsid formation systematically suppress FBNSV long-distance movement, and thus systemic infection of host plants, despite positive detection of the mutated coat protein when the corresponding segment is agroinfiltrated into plant leaves. These results strongly suggest that the viral genome does not propagate within the plant vascular system under the form of uncoated DNA molecules or DNA:coat-protein complexes, but rather moves long distance as assembled viral particles.
History
DepositionJun 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein


Theoretical massNumber of molelcules
Total (without water)19,2001
Polymers19,2001
Non-polymers00
Water0
1
A: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)1,152,02560
Polymers1,152,02560
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Capsid protein / Capsid


Mass: 19200.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Faba bean necrotic stunt virus / References: UniProt: C7DLN3

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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: Faba bean necrotic stunt virus / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Faba bean necrotic stunt virus
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Virus shellName: capsid / Triangulation number (T number): 3
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
10RELION3final Euler assignment
12RELION33D reconstruction
13PHENIX1.15.2model refinement
14Coot0.9-premodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5156 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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