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- PDB-9r7y: RNA-free helical (h9.7) virus-like particle composed of PVA coat ... -

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Basic information

Entry
Database: PDB / ID: 9r7y
TitleRNA-free helical (h9.7) virus-like particle composed of PVA coat protein with 6 mutations (H89Q, E90S, S144E, R163A, K180E, and T210R)
ComponentsGenome polyprotein
KeywordsVIRUS LIKE PARTICLE / potato virus A / virus-like particle / potyvirus / coat protein / helical
Function / homologyPotyvirus coat protein / Potyvirus coat protein / viral capsid / Genome polyprotein
Function and homology information
Biological speciesPotato virus A
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.89 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: Koritnik, N. / Kezar, A. / Kavcic, L. / Znidaric, M.T. / Leonardi, A. / De, S. / Pollari, M. / Makinen, K. / Podobnik, M.
History
DepositionMay 15, 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
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
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

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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)818,61927
Polymers818,61927
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: 30319.234 Da / Num. of mol.: 27 / Mutation: H89Q, E90S, S144E, R163A, K180E, T210R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Potato virus A / Strain: isolate Datura / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O11986
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 PVA coat protein with 6 mutations (H89Q, E90S, S144E, R163A, K180E, and T210R)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Potato virus A / Strain: isolate Datura
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: -37.08 ° / Axial rise/subunit: 3.85 Å / Axial symmetry: C1
3D reconstructionResolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 122826 / Symmetry type: HELICAL

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