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- EMDB-47498: Icosahedral Map of yPOWV -

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Basic information

Entry
Database: EMDB / ID: EMD-47498
TitleIcosahedral Map of yPOWV
Map dataComplete icosahedral map of yPOWV
Sample
  • Virus: Powassan virus
KeywordsVirus
Biological speciesPowassan virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsDas S / Hafenstein S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2025
Title: Atomic-resolution structure of a chimeric Powassan tick-borne flavivirus.
Authors: Sayan Das / Anoop Narayanan / Anqi Wang / Ibrahim M Moustafa / Sung Hyun Cho / Dana Mitzel / Joyce Jose / Susan L Hafenstein /
Abstract: Powassan virus (POWV) is an emerging tick-borne flavivirus for which no vaccine or antiviral treatment exists. The incidence of human infections of POWV in North America has been increasing because ...Powassan virus (POWV) is an emerging tick-borne flavivirus for which no vaccine or antiviral treatment exists. The incidence of human infections of POWV in North America has been increasing because of the expanding distribution of the tick vector that transmits POWV to humans. To mitigate the dangers of handling a risk group 3 human pathogen, a chimeric virus was constructed from the genetic backbone of a yellow fever virus vaccine strain 17D (YFV-17D) and the external structural proteins of POWV lineage II. The chimera had a comparable phenotype as POWV. The atomic resolution of yellow fever virus-Powassan virus chimera (yPOWV) structure was built without ambiguity, revealing surface glycans and lipid pocket factors. The similarity to other flavivirus structures and the phenotype similar to YFV-17D suggest that there could be future potential as a vaccine candidate.
History
DepositionOct 24, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47498.png

Downloads & links

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Map

FileDownload / File: emd_47498.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComplete icosahedral map of yPOWV
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 672 pix.
= 819.84 Å		1.22 Å/pix.
x 672 pix.
= 819.84 Å		1.22 Å/pix.
x 672 pix.
= 819.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.22 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.66
Minimum - Maximum-0.35164058 - 1.6408265
Average (Standard dev.)0.001788051 (±0.1297784)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions672672672
Spacing672672672
CellA=B=C: 819.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened icosahedral map of yPOWV

Fileemd_47498_additional_1.map
AnnotationSharpened icosahedral map of yPOWV
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A for icosahedral map of yPOWV

Fileemd_47498_half_map_1.map
AnnotationHalf-map A for icosahedral map of yPOWV
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B for icosahedral map of yPOWV

Fileemd_47498_half_map_2.map
AnnotationHalf-map B for icosahedral map of yPOWV
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Powassan virus

EntireName: Powassan virus
Components
  • Virus: Powassan virus

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Supramolecule #1: Powassan virus

SupramoleculeName: Powassan virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 11083 / Sci species name: Powassan virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5o6a

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53103
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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