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- PDB-9jzn: Tetrameric complex of the Borna disease virus 1 nucleoprotein (mu... -

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Basic information

Entry
Database: PDB / ID: 9jzn
TitleTetrameric complex of the Borna disease virus 1 nucleoprotein (mutant Lys164Ala)
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / nucleoprotein / 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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsGoto, S.H. / Sugita, Y. / Hirai, Y. / Horie, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and Technology21460759 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)24K02284 Japan
CitationJournal: To Be Published
Title: Tetrameric complex of Borna disease virus 1 nucleoprotein (mutant Lys164Ala)
Authors: Goto, S.H. / Sugita, Y. / Hirai, Y. / Horie, M.
History
DepositionOct 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)43,5191
Polymers43,5191
Non-polymers00
Water00
1
A: Nucleoprotein

A: Nucleoprotein

A: Nucleoprotein

A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)174,0754
Polymers174,0754
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C4 (4 fold cyclic))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-1), (1), (1)124.528
3generate(-1), (-1), (1)124.528, 124.528
4generate(1), (-1), (1)124.528

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Components

#1: Protein Nucleoprotein / N protein / Nucleocapsid protein / p38 / p40


Mass: 43518.730 Da / Num. of mol.: 1 / Mutation: K164A
Source method: isolated from a genetically manipulated source
Details: Full-length nucleoprotein (mutant Lys164Ala) of the Borna disease virus 1 strain He/80 with N-terminal expression tag
Source: (gene. exp.) Borna disease virus 1 / Strain: He/80 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C796
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Purified Borna disease virus 1 nucleoprotein (mutant Lys164Ala)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Borna disease virus 1 / Strain: He/80
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 43 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
8Cootmodel fitting
10Servalcatmodel refinement
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
13cryoSPARCclassification
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 170764 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: RECIPROCAL
Atomic model buildingPDB-ID: 1n93

1n93


Accession code: 1n93 / Source name: PDB / Type: experimental model
RefinementResolution: 3.15→112.94 Å / Cor.coef. Fo:Fc: 0.927 / SU B: 10.576 / SU ML: 0.17 / ESU R: 0.167
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.29491 --
obs0.29491 91538 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 154.477 Å2
Refinement stepCycle: 1 / Total: 2607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0090.0122664
ELECTRON MICROSCOPYr_bond_other_d0.0010.0162559
ELECTRON MICROSCOPYr_angle_refined_deg1.5031.8243608
ELECTRON MICROSCOPYr_angle_other_deg0.6911.7485912
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.2465333
ELECTRON MICROSCOPYr_dihedral_angle_2_deg6.695516
ELECTRON MICROSCOPYr_dihedral_angle_3_deg11.3310460
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.080.2412
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.023070
ELECTRON MICROSCOPYr_gen_planes_other0.0040.02584
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it22.04813.7351341
ELECTRON MICROSCOPYr_mcbond_other22.04713.7321341
ELECTRON MICROSCOPYr_mcangle_it31.32424.7231671
ELECTRON MICROSCOPYr_mcangle_other31.32924.7441672
ELECTRON MICROSCOPYr_scbond_it28.37816.4921323
ELECTRON MICROSCOPYr_scbond_other28.36916.5141324
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other43.68428.8161938
ELECTRON MICROSCOPYr_long_range_B_refined56.384316.242550
ELECTRON MICROSCOPYr_long_range_B_other56.384316.242551
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.15→3.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.377 6709 -
obs--100 %

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