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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: Das S / Narayanan A / Wang A / Moustafa IM / Cho SH / Mitzel D / Jose J / Hafenstein SL
History
DepositionOct 24, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 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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