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- EMDB-67473: Hexameric complex of the Borna disease virus 1 nucleoprotein boun... -

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Basic information

Entry
Database: EMDB / ID: EMD-67473
TitleHexameric complex of the Borna disease virus 1 nucleoprotein bound to RNA (mutant Arg341Ala)
Map dataprimary map
Sample
  • Complex: Purified Borna disease virus 1 nucleoprotein (mutant Arg341Ala)
Keywordsnucleoprotein / complex / VIRAL PROTEIN
Biological speciesBorna disease virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 7.83 Å
AuthorsSugita Y / Goto SH / Hirai Y / Horie M
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Science and Technology21460759 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)24K02284 Japan
CitationJournal: To Be Published
Title: Structure and assembly of Borna disease virus 1 nucleoprotein-RNA complexes
Authors: Sugita Y / Hirai Y / Goto SH / Horie M
History
DepositionDec 5, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_67473.png

Downloads & links

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Map

FileDownload / File: emd_67473.map.gz / Format: CCP4 / Size: 5.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.48 Å/pix.
x 114 pix.
= 168.72 Å		1.48 Å/pix.
x 114 pix.
= 168.72 Å		1.48 Å/pix.
x 114 pix.
= 168.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.48 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.19341902 - 0.51753867
Average (Standard dev.)0.0026397733 (±0.049851455)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions114114114
Spacing114114114
CellA=B=C: 168.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67473_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_67473_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_67473_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Purified Borna disease virus 1 nucleoprotein (mutant Arg341Ala)

EntireName: Purified Borna disease virus 1 nucleoprotein (mutant Arg341Ala)
Components
  • Complex: Purified Borna disease virus 1 nucleoprotein (mutant Arg341Ala)

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Supramolecule #1: Purified Borna disease virus 1 nucleoprotein (mutant Arg341Ala)

SupramoleculeName: Purified Borna disease virus 1 nucleoprotein (mutant Arg341Ala)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Borna disease virus 1 / Strain: He/80

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 14795
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9jzj


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL

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