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- EMDB-53790: Potato virus A (PVA) -

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Basic information

Entry
Database: EMDB / ID: EMD-53790
TitlePotato virus A (PVA)
Map data
Sample
  • Complex: Potato virus A (PVA)
    • Protein or peptide: Capsid protein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Keywordspotato virus A / potyvirus / coat protein / RNA / helical / VIRUS
Function / homology
Function and homology information


nuclear-inclusion-a endopeptidase / helper-component proteinase / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / host cell cytoplasmic vesicle / helical viral capsid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / symbiont-mediated suppression of host innate immune response ...nuclear-inclusion-a endopeptidase / helper-component proteinase / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / host cell cytoplasmic vesicle / helical viral capsid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / symbiont-mediated suppression of host innate immune response / viral translational frameshifting / RNA-directed RNA polymerase / 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 speciesPotato virus A
Methodhelical reconstruction / cryo EM / Resolution: 2.39 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 15, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53790.png

Downloads & links

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Map

FileDownload / File: emd_53790.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.
= 331.1 Å		0.95 Å/pix.
x 350 pix.
= 331.1 Å		0.95 Å/pix.
x 350 pix.
= 331.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.946 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.11
Minimum - Maximum-7.729389 - 12.523978
Average (Standard dev.)0.021583354 (±0.47835374)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 331.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53790_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53790_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Potato virus A (PVA)

EntireName: Potato virus A (PVA)
Components
  • Complex: Potato virus A (PVA)
    • Protein or peptide: Capsid protein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*U)-3')

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Supramolecule #1: Potato virus A (PVA)

SupramoleculeName: Potato virus A (PVA) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Potato virus A / Strain: isolate B11

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 36 / Enantiomer: LEVO
Source (natural)Organism: Potato virus A / Strain: isolate B11
Molecular weightTheoretical: 30.429461 KDa
SequenceString: AETLDASEAL AQKSEGRKKE RESNSSKAVA VKDKDVDLGT AGTHSVPRLK SMTSKLTLPM LKGKSVVNLD HLLSYKPKQV DLSNARATH EQFQNWYDGV MASYELEESS MEIILNGFMV WCIENGTSPD INGVWTMMDN EEQVSYPLKP MLDHAKPSLR Q IMRHFSAL ...String:
AETLDASEAL AQKSEGRKKE RESNSSKAVA VKDKDVDLGT AGTHSVPRLK SMTSKLTLPM LKGKSVVNLD HLLSYKPKQV DLSNARATH EQFQNWYDGV MASYELEESS MEIILNGFMV WCIENGTSPD INGVWTMMDN EEQVSYPLKP MLDHAKPSLR Q IMRHFSAL AEAYIEMRSR EKPYMPRYGL QRNLRDQSLA RYAFDFYEIT ATTPIRAKEA HLQMKAAALK NSNTNMFGLD GN VTTSEED TERHTATDVN RNMHHLLGVK GV

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: Potato virus A / Strain: isolate B11
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: 3.89 Å
Applied symmetry - Helical parameters - Δ&Phi: -40.90 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 481088
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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