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- EMDB-53450: Structure of the Plum Pox Virus (PPV) -

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Basic information

Entry
Database: EMDB / ID: EMD-53450
TitleStructure of the Plum Pox Virus (PPV)
Map datasharp
Sample
  • Virus: Plum pox virus
    • Protein or peptide: Coat Protein (CP)
    • RNA: RNA
KeywordsPotyvirus / Plum Pox Virus / PPV / VIRUS
Function / homologyPotyvirus coat protein / Potyvirus coat protein / viral capsid / Genome polyprotein
Function and homology information
Biological speciesPlum pox virus
Methodhelical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsBonnet DMV / Chaves-Sanjuan A
Funding support Italy, 1 items
OrganizationGrant numberCountry
Ministero dell Universita e della Ricerca Italy
CitationJournal: Arch Virol / Year: 2025
Title: Structural characterization of plum pox virus by cryo-electron microscopy.
Authors: Diane Marie Valérie Jeanne Bonnet / Antonio Chaves-Sanjuan / Nicoletta Contaldo / Angelo De Stradis / Rosanna Caliandro / Angelantonio Minafra / Filippo Geuna /
Abstract: Plum pox virus (PPV), a significant member of the genus Potyvirus, represents a global agricultural challenge, causing significant economic losses and threatening fruit farming due to its easy ...Plum pox virus (PPV), a significant member of the genus Potyvirus, represents a global agricultural challenge, causing significant economic losses and threatening fruit farming due to its easy transmission to most Prunus species. Here, we present the high-resolution structural characterization of PPV using cryo-electron microscopy (cryo-EM). The reconstructed structure at 2.9 Å reveals a filamentous virion with a helical assembly formed by the coat protein (CP), which encapsidates a single-stranded RNA (ssRNA) genome. The structure of the CP core shows remarkable conservation with other potyviruses, with an RNA binding site and inter-subunit interactions mediated in part by the N-terminal arm, which is confirmed here to have a disordered structure. Mass spectrometry analysis identified numerous post-translational modifications, mostly phosphorylation, primarily in the flexible N-terminal region. In silico predictions revealed intrinsically disordered regions, which is compatible with the amyloidogenic properties of the CP. These results provide new insights into the architecture and assembly of PPV, offering a basis for future studies and, possibly, antiviral strategies.
History
DepositionApr 16, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53450.png

Downloads & links

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Map

FileDownload / File: emd_53450.map.gz / Format: CCP4 / Size: 155.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharp
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 344 pix.
= 305.816 Å		0.89 Å/pix.
x 344 pix.
= 305.816 Å		0.89 Å/pix.
x 344 pix.
= 305.816 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.889 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.8
Minimum - Maximum-3.575925 - 7.4596076
Average (Standard dev.)0.030183809 (±0.38215458)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions344344344
Spacing344344344
CellA=B=C: 305.816 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53450_msk_1.map
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Additional map: #1

Fileemd_53450_additional_1.map
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Half map: #1

Fileemd_53450_half_map_1.map
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Half map: #2

Fileemd_53450_half_map_2.map
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Sample components

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Entire : Plum pox virus

EntireName: Plum pox virus
Components
  • Virus: Plum pox virus
    • Protein or peptide: Coat Protein (CP)
    • RNA: RNA

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Supramolecule #1: Plum pox virus

SupramoleculeName: Plum pox virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12211 / Sci species name: Plum pox virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / Name: CP

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Macromolecule #1: Coat Protein (CP)

MacromoleculeName: Coat Protein (CP) / type: protein_or_peptide / ID: 1 / Details: Coat Protein (CP) / Number of copies: 45 / Enantiomer: LEVO
Source (natural)Organism: Plum pox virus
Molecular weightTheoretical: 36.551996 KDa
Recombinant expressionOrganism: Plum pox virus
SequenceString: ADEREDDEEV DAGGPTVVTA PAATVATTQP APVIQPAPQT TAPMFNPIFT PATTQPAVRP VPPISGTKPR SFGVYGNEDA SPSTSNTLV NTGRDRDVDA GSIGTFTVPR LKTMTSKLSL PKVKGKAIMN LNHLAHYSPA QVDLSNTRAP QSCFQTWYEG V KRDYDVTD ...String:
ADEREDDEEV DAGGPTVVTA PAATVATTQP APVIQPAPQT TAPMFNPIFT PATTQPAVRP VPPISGTKPR SFGVYGNEDA SPSTSNTLV NTGRDRDVDA GSIGTFTVPR LKTMTSKLSL PKVKGKAIMN LNHLAHYSPA QVDLSNTRAP QSCFQTWYEG V KRDYDVTD EEMSIILNGL MVWCIENGTS PNINGMWVMM DGETQVEYPI KPLLDHAKPT FRQIMAHFSN VAEAYIEKRN YE KAYMPRY GIQRNLTDYS LARYAFDFYE MTSTTPVRAR EAHIQMKAAA LRNVQNRLFG LDGNVGTQEE DTERHTAGDV NRN MHNLLG VRGV

UniProtKB: Genome polyprotein

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Macromolecule #2: RNA

MacromoleculeName: RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Plum pox virus
Molecular weightTheoretical: 191.003562 KDa
SequenceString: UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU U UUUUUUUU ...String:
UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU U UUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UU UUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUU UUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUU UUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUU UUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUU UUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU U

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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: 7
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2508 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.08 Å
Applied symmetry - Helical parameters - Δ&Phi: -40.89 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 406769
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING ONLY
Segment selectionNumber selected: 406769 / Software - Name: RELION (ver. 3.1)
Startup modelType of model: OTHER / Details: ab initio
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9qy3:
Structure of the Plum Pox Virus (PPV)

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