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- PDB-9ra2: RNA-free stacked-ring (r9) virus-like particle composed of JGMV c... -

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Basic information

Entry
Database: PDB / ID: 9ra2
TitleRNA-free stacked-ring (r9) virus-like particle composed of JGMV coat protein
ComponentsGenome polyprotein
KeywordsVIRUS LIKE PARTICLE / Johnsongrass mosaic virus / virus-like particle / potyvirus / coat protein / helical
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
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsKoritnik, N. / Kezar, A. / Podobnik, M.
Funding support Slovenia, 1items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2026Group: Data collection / Database references / Category: citation / em_admin
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Revision 1.1Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin / Data content type: EM metadata / EM metadata / EM metadata
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Revision 1.2Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Aa: Genome polyprotein
Ab: Genome polyprotein
Ac: Genome polyprotein
Ad: Genome polyprotein
Ae: Genome polyprotein
Af: Genome polyprotein
Ag: Genome polyprotein
Ah: Genome polyprotein
Ai: Genome polyprotein
Aj: Genome polyprotein
Ak: Genome polyprotein
Al: Genome polyprotein
Am: Genome polyprotein
An: Genome polyprotein
Ao: Genome polyprotein
Ap: Genome polyprotein
Aq: Genome polyprotein
Ar: Genome polyprotein
As: Genome polyprotein
At: Genome polyprotein
Au: Genome polyprotein
Av: Genome polyprotein
Aw: Genome polyprotein
Ax: Genome polyprotein
Ay: Genome polyprotein
Az: Genome polyprotein
Ba: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)906,61527
Polymers906,61527
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Genome polyprotein


Mass: 33578.328 Da / Num. of mol.: 27
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Johnsongrass mosaic virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q82933
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Virus-like particle composed of JGMV coat protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Johnsongrass mosaic virus
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameCategory
2EPUimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 14.89 ° / Axial rise/subunit: 42.79 Å / Axial symmetry: C9
3D reconstructionResolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 271709 / Symmetry type: HELICAL

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