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- EMDB-53645: RNA-free stacked-ring (r8) virus-like particle composed of PVY co... -

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Basic information

Entry
Database: EMDB / ID: EMD-53645
TitleRNA-free stacked-ring (r8) virus-like particle composed of PVY coat protein with R208T mutation
Map data
Sample
  • Complex: RNA-free stacked-ring (r8) virus-like particle composed of PVY coat protein with R208T mutation
    • Protein or peptide: Capsid protein
Keywordspotato virus Y / virus-like particle / potyvirus / coat protein / helical / VIRUS LIKE PARTICLE
Biological speciesPotato virus Y strain NTN / Potato virus A
Methodhelical reconstruction / cryo EM / Resolution: 3.86 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 12, 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_53645.png

Downloads & links

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Map

FileDownload / File: emd_53645.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: 0.492
Minimum - Maximum-0.9498135 - 1.9130087
Average (Standard dev.)0.011194367 (±0.0932123)
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_53645_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_53645_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 : RNA-free stacked-ring (r8) virus-like particle composed of PVY co...

EntireName: RNA-free stacked-ring (r8) virus-like particle composed of PVY coat protein with R208T mutation
Components
  • Complex: RNA-free stacked-ring (r8) virus-like particle composed of PVY coat protein with R208T mutation
    • Protein or peptide: Capsid protein

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Supramolecule #1: RNA-free stacked-ring (r8) virus-like particle composed of PVY co...

SupramoleculeName: RNA-free stacked-ring (r8) virus-like particle composed of PVY coat protein with R208T mutation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Potato virus Y strain NTN

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Potato virus A
SequenceString: GNDTIDAGGS TKKDAKQEQG SIQPNLNKEK EKDVNVGTSG THTVPRIKAI TSKMRMPKSK GATVLNLEHL LEYAPQQIDI SNTRATQSQF DTWYEAVQLA YDIGETEMPT VMNGLMVWCI ENGTSPNING VWVMMDGDEQ VEYPLKPIVE NAKPTLRQIM AHFSDVAEAY ...String:
GNDTIDAGGS TKKDAKQEQG SIQPNLNKEK EKDVNVGTSG THTVPRIKAI TSKMRMPKSK GATVLNLEHL LEYAPQQIDI SNTRATQSQF DTWYEAVQLA YDIGETEMPT VMNGLMVWCI ENGTSPNING VWVMMDGDEQ VEYPLKPIVE NAKPTLRQIM AHFSDVAEAY IEMRNKKEPY MPRYGLVRNL RDGSLARYAF DFYEVTSTTP VRAREAHIQM KAAALKSAQS RLFGLDGGIS TQEENTERHT TEDVSPSMHT LLGVKNM

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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 / Pretreatment - Type: GLOW DISCHARGE
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: 43.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 14.36 °
Applied symmetry - Helical parameters - Axial symmetry: C8 (8 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 16689
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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