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- EMDB-53645: RNA-free stacked-ring (r8) virus-like particle composed of PVY co... -

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Basic information

Entry
Database: EMDB / ID: EMD-53645
TitleRNA-free stacked-ring (r8) virus-like particle composed of PVY coat protein with R208T mutation
Map data
Sample
  • Complex: RNA-free stacked-ring (r8) virus-like particle composed of PVY coat protein with R208T mutation
    • Protein or peptide: Capsid protein
Keywordspotato virus Y / virus-like particle / potyvirus / coat protein / helical / VIRUS LIKE PARTICLE
Biological speciesPotato virus Y strain NTN / Potato virus A
Methodhelical reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsKoritnik N / Kezar A / Podobnik M
Funding support Slovenia, 1 items
OrganizationGrant numberCountry
Slovenian Research Agency Slovenia
CitationJournal: Commun Biol / Year: 2026
Title: Species-specific structural adaptation of the potyviral coat protein in virions and virus-like particles.
Authors: Neža Koritnik / Andreja Kežar / Luka Kavčič / Magda Tušek Žnidarič / Adrijana Leonardi / Swarnalok De / Maija Pollari / Kristiina Mäkinen / Marjetka Podobnik /
Abstract: Potyviruses are the largest group of plant positive-sense single-stranded RNA viruses and represent a major economic burden worldwide. Their coat protein (CP) forms a filamentous, flexible capsid ...Potyviruses are the largest group of plant positive-sense single-stranded RNA viruses and represent a major economic burden worldwide. Their coat protein (CP) forms a filamentous, flexible capsid around the genomic RNA. However, information is still lacking on the mechanisms of virion assembly, disassembly and stability, which is central to understanding virus biology and control. Here, we investigate the role of CP in these processes using structural, biochemical and biophysical studies of five potyviral CPs from three phylogenetic clades combined with bioinformatics and in planta experiments. Our results suggest that, while potyviruses have a conserved virion structure, the amino acids forming the CP-CP and CP-RNA interactions leading to this structure are species-specific. We show that the species-specific CP sequence also determines the architecture of RNA-free virus-like particles (VLPs) and the degree of their structural polymorphism. We identify the residues that determine this specificity at distinct S1-S4 interaction sites. In contrast, a highly conserved charged amino acid triad at the CP-CP interface is essential for the stability of virions and RNA-free VLPs. These results contribute to understanding the molecular mechanism of potyviral virion assembly and highlight the significance of the amino acid sequence of selected CPs in potential biotechnological or biomedical applications.
History
DepositionMay 12, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53645.png

Downloads & links

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Map

FileDownload / File: emd_53645.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 350 pix.
= 332.5 Å		0.95 Å/pix.
x 350 pix.
= 332.5 Å		0.95 Å/pix.
x 350 pix.
= 332.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.492
Minimum - Maximum-0.9498135 - 1.9130087
Average (Standard dev.)0.011194367 (±0.0932123)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 332.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_53645_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53645_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : RNA-free stacked-ring (r8) virus-like particle composed of PVY co...

EntireName: RNA-free stacked-ring (r8) virus-like particle composed of PVY coat protein with R208T mutation
Components
  • Complex: RNA-free stacked-ring (r8) virus-like particle composed of PVY coat protein with R208T mutation
    • Protein or peptide: Capsid protein

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Supramolecule #1: RNA-free stacked-ring (r8) virus-like particle composed of PVY co...

SupramoleculeName: RNA-free stacked-ring (r8) virus-like particle composed of PVY coat protein with R208T mutation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Potato virus Y strain NTN

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Potato virus A
SequenceString: GNDTIDAGGS TKKDAKQEQG SIQPNLNKEK EKDVNVGTSG THTVPRIKAI TSKMRMPKSK GATVLNLEHL LEYAPQQIDI SNTRATQSQF DTWYEAVQLA YDIGETEMPT VMNGLMVWCI ENGTSPNING VWVMMDGDEQ VEYPLKPIVE NAKPTLRQIM AHFSDVAEAY ...String:
GNDTIDAGGS TKKDAKQEQG SIQPNLNKEK EKDVNVGTSG THTVPRIKAI TSKMRMPKSK GATVLNLEHL LEYAPQQIDI SNTRATQSQF DTWYEAVQLA YDIGETEMPT VMNGLMVWCI ENGTSPNING VWVMMDGDEQ VEYPLKPIVE NAKPTLRQIM AHFSDVAEAY IEMRNKKEPY MPRYGLVRNL RDGSLARYAF DFYEVTSTTP VRAREAHIQM KAAALKSAQS RLFGLDGGIS TQEENTERHT TEDVSPSMHT LLGVKNM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 150000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 43.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 14.36 °
Applied symmetry - Helical parameters - Axial symmetry: C8 (8 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 16689
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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