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- PDB-6scl: Cryo-EM Structure of Barley Yellow Dwarf Virus VLP -

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Basic information

Entry
Database: PDB / ID: 6scl
TitleCryo-EM Structure of Barley Yellow Dwarf Virus VLP
ComponentsCoat protein
KeywordsVIRUS LIKE PARTICLE / Luteovirus / VLP / Capsid.
Function / homologyLuteovirus group 1 coat protein / Luteovirus coat protein / Viral coat protein subunit / viral capsid / structural molecule activity / Coat protein
Function and homology information
Biological speciesBarley yellow dwarf virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsByrne, M.J. / Ranson, N.A.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/R00160X/1 United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L014130/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J004596/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBBS/E/000PR9794 United Kingdom
CitationJournal: Structure / Year: 2019
Title: Combining Transient Expression and Cryo-EM to Obtain High-Resolution Structures of Luteovirid Particles.
Authors: Matthew J Byrne / John F C Steele / Emma L Hesketh / Miriam Walden / Rebecca F Thompson / George P Lomonossoff / Neil A Ranson /
Abstract: The Luteoviridae are pathogenic plant viruses responsible for significant crop losses worldwide. They infect a wide range of food crops, including cereals, legumes, cucurbits, sugar beet, sugarcane, ...The Luteoviridae are pathogenic plant viruses responsible for significant crop losses worldwide. They infect a wide range of food crops, including cereals, legumes, cucurbits, sugar beet, sugarcane, and potato and, as such, are a major threat to global food security. Viral replication is strictly limited to the plant vasculature, and this phloem limitation, coupled with the need for aphid transmission of virus particles, has made it difficult to generate virus in the quantities needed for high-resolution structural studies. Here, we exploit recent advances in heterologous expression in plants to produce sufficient quantities of virus-like particles for structural studies. We have determined their structures to high resolution by cryoelectron microscopy, providing the molecular-level insight required to rationally interrogate luteovirid capsid formation and aphid transmission, thereby providing a platform for the development of preventive agrochemicals for this important family of plant viruses.
History
DepositionJul 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2Dec 11, 2019Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

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Assembly

Deposited unit
A: Coat protein
C: Coat protein
B: Coat protein


Theoretical massNumber of molelcules
Total (without water)66,2503
Polymers66,2503
Non-polymers00
Water0
1
A: Coat protein
C: Coat protein
B: Coat protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,974,972180
Polymers3,974,972180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
MethodPISA

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Components

#1: Protein Coat protein


Mass: 22083.176 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Barley yellow dwarf virus / Gene: cp / Production host: Nicotiana benthamiana (plant) / References: UniProt: O56812

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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: Barley yellow dwarf virus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Barley yellow dwarf virus
Source (recombinant)Organism: Nicotiana benthamiana (plant)
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.4
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: 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: 63.2 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategory
1RELION2.1particle selection
4GctfCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
13RELION2.13D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 324235 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0083315
ELECTRON MICROSCOPYf_angle_d0.9334470
ELECTRON MICROSCOPYf_dihedral_angle_d13.1851977
ELECTRON MICROSCOPYf_chiral_restr0.061518
ELECTRON MICROSCOPYf_plane_restr0.006560

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