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- EMDB-10142: Cryo-EM Structure of Barley Yellow Dwarf Virus VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-10142
TitleCryo-EM Structure of Barley Yellow Dwarf Virus VLP
Map dataElectron density map for Barley Yellow Dwarf Virus VLP.
Sample
  • Virus: Barley yellow dwarf virus
    • Protein or peptide: Coat protein
KeywordsLuteovirus / VLP / Capsid. / VIRUS LIKE PARTICLE
Function / homologyLuteovirus group 1 coat protein / Luteovirus coat protein / T=3 icosahedral viral capsid / Viral coat protein subunit / structural molecule activity / Coat protein
Function and homology information
Biological speciesBarley yellow dwarf virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsByrne MJ / Ranson NA
Funding support United Kingdom, 5 items
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, 2019-
Header (metadata) releaseOct 2, 2019-
Map releaseOct 2, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6scl
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6scl
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10142.png

Downloads & links

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Map

FileDownload / File: emd_10142.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationElectron density map for Barley Yellow Dwarf Virus VLP.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 384 pix.
= 408.96 Å		1.07 Å/pix.
x 384 pix.
= 408.96 Å		1.07 Å/pix.
x 384 pix.
= 408.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.19003971 - 0.27505687
Average (Standard dev.)0.0024278294 (±0.016245374)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 408.96002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z408.960408.960408.960
α/β/γ90.00090.00090.000
start NX/NY/NZ-31-35-52
NX/NY/NZ11798209
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.1900.2750.002

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Supplemental data

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Sample components

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Entire : Barley yellow dwarf virus

EntireName: Barley yellow dwarf virus
Components
  • Virus: Barley yellow dwarf virus
    • Protein or peptide: Coat protein

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Supramolecule #1: Barley yellow dwarf virus

SupramoleculeName: Barley yellow dwarf virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12037 / Sci species name: Barley yellow dwarf virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Barley yellow dwarf virus
Molecular weightTheoretical: 22.083176 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MNSVGRRGPR RANQNGTRRR RRRTVRPVVV VQPNRAGPRR RNGRRKGRGG ANFVFRPTGG TEVFVFSVDN LKANSSGAIK FGPSLSQCP ALSDGILKSY HRYKITSIRV EFKSHASANT AGAIFIELDT ACKQSALGSY INSFTISKTA SKTFRSEAIN G KEFQESTI ...String:
MNSVGRRGPR RANQNGTRRR RRRTVRPVVV VQPNRAGPRR RNGRRKGRGG ANFVFRPTGG TEVFVFSVDN LKANSSGAIK FGPSLSQCP ALSDGILKSY HRYKITSIRV EFKSHASANT AGAIFIELDT ACKQSALGSY INSFTISKTA SKTFRSEAIN G KEFQESTI DQFWMLYKAN GTTTDTAGQF IITMSVSLMT AK

UniProtKB: Coat protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 63.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 324235
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

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

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