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- EMDB-12879: Structure of Alternanthera Mosaic VLP by cryoEM -

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Basic information

Entry
Database: EMDB / ID: EMD-12879
TitleStructure of Alternanthera Mosaic VLP by cryoEM
Map dataAlternanthera mosaic VLP
Sample
  • Virus: Alternanthera mosaic virus
    • Protein or peptide: Coat protein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
KeywordsPotexvirus / Virus Like Particle / VLP.
Function / homologyPotexviruses and carlaviruses coat protein signature. / Potex/carlavirus coat protein / Viral coat protein / helical viral capsid / ribonucleoprotein complex / structural molecule activity / Coat protein
Function and homology information
Biological speciesAlternanthera mosaic virus
Methodhelical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsByrne MJ / Ranson NA
Funding support United Kingdom, 1 items
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, 2021-
Header (metadata) releaseJun 23, 2021-
Map releaseJun 23, 2021-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.046
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.046
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7og6
  • Surface level: 0.046
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7og6
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12879.png

Downloads & links

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Map

FileDownload / File: emd_12879.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAlternanthera mosaic VLP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 208 pix.
= 221.52 Å		1.07 Å/pix.
x 208 pix.
= 221.52 Å		1.07 Å/pix.
x 208 pix.
= 221.52 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: 0.046 / Movie #1: 0.046
Minimum - Maximum-0.028382033 - 0.12481764
Average (Standard dev.)0.0016171017 (±0.018317087)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 221.52002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z208208208
origin x/y/z0.0000.0000.000
length x/y/z221.520221.520221.520
α/β/γ90.00090.00090.000
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS208208208
D min/max/mean-0.0280.1250.002

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Supplemental data

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Sample components

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Entire : Alternanthera mosaic virus

EntireName: Alternanthera mosaic virus
Components
  • Virus: Alternanthera mosaic virus
    • Protein or peptide: Coat protein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*U)-3')

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Supramolecule #1: Alternanthera mosaic virus

SupramoleculeName: Alternanthera mosaic virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 85454 / Sci species name: Alternanthera mosaic virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Alternanthera mosaic virus
Molecular weightTheoretical: 22.243895 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MSTPFPQVTQ EQMNAFTPHT TSNLLPSPEQ LTTIANLLVA AKVPAASTTT IALELVNFCY DNGSSTYTAV VGPSSLAEVS LSQVANIVK ASGTSLRKFC RFFAPIIWNL RTDKTPPANW EANGFKPTEK FAAFDFFDGV ENPAAMQPPG GLVRTPSQAE R IANATNKQ ...String:
MSTPFPQVTQ EQMNAFTPHT TSNLLPSPEQ LTTIANLLVA AKVPAASTTT IALELVNFCY DNGSSTYTAV VGPSSLAEVS LSQVANIVK ASGTSLRKFC RFFAPIIWNL RTDKTPPANW EANGFKPTEK FAAFDFFDGV ENPAAMQPPG GLVRTPSQAE R IANATNKQ VNLFQAAAQD NNFASNSAFI TKGQLSSNSP TIQYLPPPE

UniProtKB: Coat protein

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Macromolecule #2: RNA (5'-R(P*UP*UP*UP*UP*U)-3')

MacromoleculeName: RNA (5'-R(P*UP*UP*UP*UP*U)-3') / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Alternanthera mosaic virus
Molecular weightTheoretical: 1.485872 KDa
SequenceString:
UUUUU

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8 / Details: 10 mM Tris-HCl, pH 8.0
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 1.11 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

Final reconstructionApplied symmetry - Helical parameters - Δz: 3.959 Å
Applied symmetry - Helical parameters - Δ&Phi: 41.11 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 32018
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE

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