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- EMDB-61933: Hexameric flat ring-like complex of the Borna disease virus 1 nuc... -

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Basic information

Entry
Database: EMDB / ID: EMD-61933
TitleHexameric flat ring-like complex of the Borna disease virus 1 nucleoprotein (mutant Lys164Ala)
Map data
Sample
  • Complex: Purified Borna disease virus 1 nucleoprotein (mutant Lys164Ala)
    • Protein or peptide: Nucleoprotein of the Borna disease virus 1 (mutant Lys164Ala)
Keywordsnucleoprotein / complex / VIRAL PROTEIN
Biological speciesBorna disease virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 6.26 Å
AuthorsGoto SH / Sugita Y / 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: Sci Adv / Year: 2026
Title: Structure and assembly of Borna disease virus 1 nucleoprotein-RNA complexes.
Authors: Yukihiko Sugita / Yuya Hirai / Shinya H Goto / Takuro Fujiwara / Keizo Tomonaga / Takeshi Noda / Masayuki Horie /
Abstract: Structures of nucleoprotein (N)-RNA complexes of the , a virus family in the order , have not been reported. Here, using cryo-electron microscopy (cryo-EM), we report high-resolution structures of ...Structures of nucleoprotein (N)-RNA complexes of the , a virus family in the order , have not been reported. Here, using cryo-electron microscopy (cryo-EM), we report high-resolution structures of Borna disease virus 1 (BoDV-1) N-RNA complex assemblies, including a dominant hexameric ring-like complex and less populated heptameric and octameric forms, the first RNA-bound N structures reported from this family. These structures reveal key features of N-RNA engagement and a BoDV-1-specific stoichiometry of eight nucleotides per N, providing a framework for comparison with related negative-strand RNA viruses. In addition to these RNA-bound complexes, we identified multiple RNA-free oligomers, indicating substantial conformational flexibility of N. Mutational analyses identified residues essential for nucleocapsid formation and RNA synthesis. Cryo-EM of mutant complexes captured RNA-free assemblies, suggesting that initial N oligomerization precedes RNA binding. These findings clarify the structural organization of the N-RNA complex and suggest how oligomeric plasticity contributes to nucleocapsid assembly.
History
DepositionOct 14, 2024-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61933.png

Downloads & links

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Map

FileDownload / File: emd_61933.map.gz / Format: CCP4 / Size: 7.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.45 Å/pix.
x 126 pix.
= 182.448 Å		1.45 Å/pix.
x 126 pix.
= 182.448 Å		1.45 Å/pix.
x 126 pix.
= 182.448 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.448 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.178
Minimum - Maximum-0.3589134 - 0.6986827
Average (Standard dev.)0.0016054417 (±0.05454579)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions126126126
Spacing126126126
CellA=B=C: 182.448 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61933_msk_1.map
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Half map: #1

Fileemd_61933_half_map_1.map
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Half map: #2

Fileemd_61933_half_map_2.map
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Sample components

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Entire : Purified Borna disease virus 1 nucleoprotein (mutant Lys164Ala)

EntireName: Purified Borna disease virus 1 nucleoprotein (mutant Lys164Ala)
Components
  • Complex: Purified Borna disease virus 1 nucleoprotein (mutant Lys164Ala)
    • Protein or peptide: Nucleoprotein of the Borna disease virus 1 (mutant Lys164Ala)

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Supramolecule #1: Purified Borna disease virus 1 nucleoprotein (mutant Lys164Ala)

SupramoleculeName: Purified Borna disease virus 1 nucleoprotein (mutant Lys164Ala)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Borna disease virus 1 / Strain: He/80

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Macromolecule #1: Nucleoprotein of the Borna disease virus 1 (mutant Lys164Ala)

MacromoleculeName: Nucleoprotein of the Borna disease virus 1 (mutant Lys164Ala)
type: protein_or_peptide / ID: 1
Details: Full-length nucleoprotein (mutant Lys164Ala) of the Borna disease virus 1 strain He/80 with N-terminal hexahistidine tag
Enantiomer: LEVO
Source (natural)Organism: Borna disease virus 1 / Strain: He/80
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MLE MPPKRR LVDDADAMED QDLYEPPASL PKLPGKFLQY TVGGSDPHPG IGHEKDIRQN AVAL LDQSR RDMFHTVTPS LVFLCLLIPG LHAAFVHGGV PRESYLSTPV TRGEQTVVKT AKFYG EKTT QRDLTELEIS SIFSHCCSLL ...String:
MGSSHHHHHH SSGLVPRGSH MLE MPPKRR LVDDADAMED QDLYEPPASL PKLPGKFLQY TVGGSDPHPG IGHEKDIRQN AVAL LDQSR RDMFHTVTPS LVFLCLLIPG LHAAFVHGGV PRESYLSTPV TRGEQTVVKT AKFYG EKTT QRDLTELEIS SIFSHCCSLL IGVVIGSSSK IKAGAEQIKA RFKTMMAALN RPSHGE TAT LLQMFNPHEA IDWINGQPWV GSFVLSLLTT DFESPGKEFM DQIKLVASYA QMTTYTT IK EYLAECMDAT LTIPVVAYEI RDFLEVSAKL KEEHADLFPF LGAIRHPDAI KLAPRSFP N LASAAFYWSK KENPTMAGYR ASTIQPGASV KETQLARYRR REISRGEDGA ELSGEISAI MRMIGVTGLN

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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: 43.0 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: 1.6 µm / Nominal defocus min: 0.6 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: 6.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 69842
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:

1n93


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

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