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- EMDB-61917: Hexameric ring-like complex of the Borna disease virus 1 nucleopr... -

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Basic information

Entry
Database: EMDB / ID: EMD-61917
TitleHexameric ring-like complex of the Borna disease virus 1 nucleoprotein bound to RNA
Map dataprimary map
Sample
  • Complex: Nucleoprotein-RNA complex of the Borna disease virus 1
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
Keywordsnucleoprotein / complex / VIRAL PROTEIN / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


symbiont-mediated arrest of host cell cycle during G2/M transition / helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / symbiont entry into host cell / host cell nucleus
Similarity search - Function
P40 nucleoprotein, Borna disease virus / P40 nucleoprotein, subdomain 1, Borna disease virus / P40 nucleoprotein superfamily, Borna disease virus / Borna disease virus P40 protein / P40 nucleoprotein, subdomain 2, Borna disease virus
Similarity search - Domain/homology
Biological speciesBorna disease virus 1 / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsSugita 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: To Be Published
Title: Tetrameric nucleoprotein complex of the Borna disease virus 1 nucleoprotein (3D class 1)
Authors: Sugita Y / Hirai Y / Horie M
History
DepositionOct 14, 2024-
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_61917.png

Downloads & links

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Map

FileDownload / File: emd_61917.map.gz / Format: CCP4 / Size: 8 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.)
1.19 Å/pix.
x 128 pix.
= 152.832 Å		1.19 Å/pix.
x 128 pix.
= 152.832 Å		1.19 Å/pix.
x 128 pix.
= 152.832 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.194 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.52683634 - 1.1338578
Average (Standard dev.)0.00424583 (±0.089080796)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 152.832 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61917_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_61917_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_61917_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 : Nucleoprotein-RNA complex of the Borna disease virus 1

EntireName: Nucleoprotein-RNA complex of the Borna disease virus 1
Components
  • Complex: Nucleoprotein-RNA complex of the Borna disease virus 1
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')

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Supramolecule #1: Nucleoprotein-RNA complex of the Borna disease virus 1

SupramoleculeName: Nucleoprotein-RNA complex of the Borna disease virus 1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Borna disease virus 1

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Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1
Details: Full-length nucleoprotein of the Borna disease virus 1 strain He/80 with N-terminal hexahistidine tag
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Borna disease virus 1 / Strain: He/80
Molecular weightTheoretical: 43.576832 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MLEMPPKRRL VDDADAMEDQ DLYEPPASLP KLPGKFLQYT VGGSDPHPGI GHEKDIRQNA VALLDQSRR DMFHTVTPSL VFLCLLIPGL HAAFVHGGVP RESYLSTPVT RGEQTVVKTA KFYGEKTTQR DLTELEISSI F SHCCSLLI ...String:
MGSSHHHHHH SSGLVPRGSH MLEMPPKRRL VDDADAMEDQ DLYEPPASLP KLPGKFLQYT VGGSDPHPGI GHEKDIRQNA VALLDQSRR DMFHTVTPSL VFLCLLIPGL HAAFVHGGVP RESYLSTPVT RGEQTVVKTA KFYGEKTTQR DLTELEISSI F SHCCSLLI GVVIGSSSKI KAGAEQIKKR FKTMMAALNR PSHGETATLL QMFNPHEAID WINGQPWVGS FVLSLLTTDF ES PGKEFMD QIKLVASYAQ MTTYTTIKEY LAECMDATLT IPVVAYEIRD FLEVSAKLKE EHADLFPFLG AIRHPDAIKL APR SFPNLA SAAFYWSKKE NPTMAGYRAS TIQPGASVKE TQLARYRRRE ISRGEDGAEL SGEISAIMRM IGVTGLN

UniProtKB: Nucleoprotein

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Macromolecule #2: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP...

MacromoleculeName: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
type: rna / ID: 2 / Details: non-specific RNA / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 7.303023 KDa
SequenceString:
UUUUUUUUUU UUUUUUUUUU UUUU

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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 KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.056 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 10212934
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 242869
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Avg.num./class: 161319 / 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
Output model

PDB-9jzl:
Hexameric ring-like complex of the Borna disease virus 1 nucleoprotein bound to RNA

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