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- EMDB-10144: Cryo-EM Structure of Potato Leaf Roll Virus VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-10144
TitleCryo-EM Structure of Potato Leaf Roll Virus VLP
Map dataCryo-EM density map for Potato Leaf Roll Virus VLP
Sample
  • Virus: Potato leafroll virus
    • Protein or peptide: Coat protein
Function / homologyLuteovirus group 1 coat protein / Luteovirus coat protein / T=3 icosahedral viral capsid / Viral coat protein subunit / viral capsid / structural molecule activity / Major capsid protein / Coat protein
Function and homology information
Biological speciesPotato leafroll virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsByrne MJ / Ranson NA
Funding support United Kingdom, 5 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/R00160X/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L014130/1 United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
Biotechnology and Biological Sciences Research CouncilBBS/E/000PR9794 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J004596/1 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 25, 2019-
Header (metadata) releaseOct 2, 2019-
Map releaseOct 2, 2019-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6sco
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6sco
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10144.png

Downloads & links

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Map

FileDownload / File: emd_10144.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM density map for Potato Leaf Roll Virus VLP
Voxel sizeX=Y=Z: 1.066 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.06663784 - 0.14466028
Average (Standard dev.)0.0018526487 (±0.0092930235)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 409.344 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0661.0661.066
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z409.344409.344409.344
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-0.0670.1450.002

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Supplemental data

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Sample components

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Entire : Potato leafroll virus

EntireName: Potato leafroll virus
Components
  • Virus: Potato leafroll virus
    • Protein or peptide: Coat protein

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Supramolecule #1: Potato leafroll virus

SupramoleculeName: Potato leafroll virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12045 / Sci species name: Potato leafroll virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host systemOrganism: Nicotiana benthamiana (plant)

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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: Potato leafroll virus
Molecular weightTheoretical: 23.193391 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MSTVVVKGNV NGGVQQPRMR RRQSLRRRAN RVQPVVMVTA PGQPRRRRRR RGGNRRSRRT GVPRGRGSSE TFVFTKDNLV GNTQGSFTF GPSLSDCPAF KDGILKAYHE YKITSILLQF VSEASSTSSG SIAYELDPHC KVSSLQSYVN KFQITKGGAK T YQARMING ...String:
MSTVVVKGNV NGGVQQPRMR RRQSLRRRAN RVQPVVMVTA PGQPRRRRRR RGGNRRSRRT GVPRGRGSSE TFVFTKDNLV GNTQGSFTF GPSLSDCPAF KDGILKAYHE YKITSILLQF VSEASSTSSG SIAYELDPHC KVSSLQSYVN KFQITKGGAK T YQARMING VEWHDSSEDQ CRILWKGNGK SSDSAGSFRV TIKVALQNPK

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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: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 71.65 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 74157
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-6sco:
Cryo-EM Structure of Potato Leaf Roll Virus VLP

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