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- EMDB-53865: ssRNA-containing helical virus-like particle composed of JGMV coa... -

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Basic information

Entry
Database: EMDB / ID: EMD-53865
TitlessRNA-containing helical virus-like particle composed of JGMV coat protein
Map data
Sample
  • Complex: Virus-like particle composed of JGMV coat protein
    • Protein or peptide: Genome polyprotein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
KeywordsJohnsongrass mosaic virus / virus-like particle / potyvirus / coat protein / helical / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / host cell cytoplasmic vesicle / helical viral capsid / helicase activity / symbiont-mediated suppression of host innate immune response / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / host cell nucleus ...hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / host cell cytoplasmic vesicle / helical viral capsid / helicase activity / symbiont-mediated suppression of host innate immune response / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding
Similarity search - Function
Helper component proteinase / Peptidase S30, polyprotein P1, potyvirus / Polyprotein, Potyviridae / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain / Potyviral polyprotein protein 3 / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain superfamily / Helper component proteinase / Peptidase family C4 / Potyvirus P1 protease / Potyviridae polyprotein ...Helper component proteinase / Peptidase S30, polyprotein P1, potyvirus / Polyprotein, Potyviridae / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain / Potyviral polyprotein protein 3 / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain superfamily / Helper component proteinase / Peptidase family C4 / Potyvirus P1 protease / Potyviridae polyprotein / Protein P3 of Potyviral polyprotein / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain profile. / Potyviridae P1 protease domain profile. / Potyvirus NIa protease (NIa-pro) domain / Potyvirus NIa protease (NIa-pro) domain profile. / Potyvirus coat protein / Potyvirus coat protein / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesJohnsongrass mosaic virus
Methodhelical reconstruction / cryo EM / Resolution: 3.4 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 20, 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_53865.png

Downloads & links

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Map

FileDownload / File: emd_53865.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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: 1.34
Minimum - Maximum-1.360029 - 3.2770844
Average (Standard dev.)0.05989308 (±0.23877108)
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_53865_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_53865_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Virus-like particle composed of JGMV coat protein

EntireName: Virus-like particle composed of JGMV coat protein
Components
  • Complex: Virus-like particle composed of JGMV coat protein
    • Protein or peptide: Genome polyprotein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*U)-3')

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Supramolecule #1: Virus-like particle composed of JGMV coat protein

SupramoleculeName: Virus-like particle composed of JGMV coat protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Johnsongrass mosaic virus

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Macromolecule #1: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 36 / Enantiomer: LEVO
Source (natural)Organism: Johnsongrass mosaic virus
Molecular weightTheoretical: 33.578328 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SGNEDAGKQK SATPAANQTA SGDGKPVQTT ATADNKPSSD NTSNAQGTSQ TKGGGESGGT NATATKKDKD VDVGSTGTFV IPKLKKVSP KMRLPMVSNK AILNLDHLIQ YKPDQRDISN ARATHTQFQF WYNRVKKEYD VDDEQMRILM NGLMVWCIEN G TSPDINGY ...String:
SGNEDAGKQK SATPAANQTA SGDGKPVQTT ATADNKPSSD NTSNAQGTSQ TKGGGESGGT NATATKKDKD VDVGSTGTFV IPKLKKVSP KMRLPMVSNK AILNLDHLIQ YKPDQRDISN ARATHTQFQF WYNRVKKEYD VDDEQMRILM NGLMVWCIEN G TSPDINGY WTMVDGNNQS EFPLKPIVEN AKPTLRQCMM HFSDAAEAYI EMRNLDEPYM PRYGLLRNLN DKSLARYAFD FY EINSRTP NRAREAHAQM KAAAIRGSTN HMFGLDGNVG ESSENTERHT AADVSRNVHS YRGAKI

UniProtKB: Genome polyprotein

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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: 36
Source (natural)Organism: Johnsongrass 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

Concentration1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
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: 4.03 Å
Applied symmetry - Helical parameters - Δ&Phi: -40.95 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 31352
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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