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- EMDB-53867: RNA-free helical (h9.6) virus-like particle composed of JGMV coat... -

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Basic information

Entry
Database: EMDB / ID: EMD-53867
TitleRNA-free helical (h9.6) 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
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: 4.02 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: Koritnik N / Kezar A / Kavcic L / Znidaric MT / Leonardi A / De S / Pollari M / Makinen K / Podobnik M
History
DepositionMay 20, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53867.png

Downloads & links

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Map

FileDownload / File: emd_53867.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: 0.88
Minimum - Maximum-2.373997 - 3.614439
Average (Standard dev.)0.021230891 (±0.16957891)
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_53867_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_53867_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

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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: 27 / 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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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: 4.5 Å
Applied symmetry - Helical parameters - Δ&Phi: -37.65 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 81832
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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