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- PDB-9jzl: Hexameric ring-like complex of the Borna disease virus 1 nucleopr... -

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Basic information

Entry
Database: PDB / ID: 9jzl
TitleHexameric ring-like complex of the Borna disease virus 1 nucleoprotein bound to RNA
Components
  • Nucleoprotein
  • 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')
KeywordsVIRAL PROTEIN/RNA / nucleoprotein / 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
RNA / RNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesBorna disease virus 1
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsSugita, 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 nucleoprotein complex of the Borna disease virus 1 nucleoprotein (3D class 1)
Authors: 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
B: Nucleoprotein
C: Nucleoprotein
R: 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')


Theoretical massNumber of molelcules
Total (without water)138,0344
Polymers138,0344
Non-polymers00
Water00
1
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
R: 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')

A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
R: 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')


Theoretical massNumber of molelcules
Total (without water)276,0678
Polymers276,0678
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
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: C2 (2 fold cyclic))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-1), (-1), (1)152.8686, 152.8686

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Components

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


Mass: 43576.832 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Full-length nucleoprotein of the Borna disease virus 1 strain He/80 with N-terminal hexahistidine tag
Source: (gene. exp.) Borna disease virus 1 / Strain: He/80 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C796
#2: RNA chain 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')


Mass: 7303.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: non-specific RNA / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
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: Nucleoprotein-RNA complex of the Borna disease virus 1
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Borna disease virus 1
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 0.056 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
1Topazparticle selection
2SerialEMimage 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
Particle selectionNum. of particles selected: 10212934
3D reconstructionResolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 242869 / 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: 3.21→145.7 Å / Cor.coef. Fo:Fc: 0.959 / SU B: 13.212 / SU ML: 0.211 / ESU R: 0.236
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.26781 --
obs0.26781 145293 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 136.798 Å2
Refinement stepCycle: 1 / Total: 8422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.0128646
ELECTRON MICROSCOPYr_bond_other_d00.0168015
ELECTRON MICROSCOPYr_angle_refined_deg1.4961.82811802
ELECTRON MICROSCOPYr_angle_other_deg0.6911.74618566
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.1715.5081131
ELECTRON MICROSCOPYr_dihedral_angle_2_deg9.234551
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.954101410
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0830.21361
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.029608
ELECTRON MICROSCOPYr_gen_planes_other0.0030.021870
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_it19.98212.7734082
ELECTRON MICROSCOPYr_mcbond_other19.97912.7734082
ELECTRON MICROSCOPYr_mcangle_it28.58422.9785092
ELECTRON MICROSCOPYr_mcangle_other28.58122.9795093
ELECTRON MICROSCOPYr_scbond_it22.214.2124564
ELECTRON MICROSCOPYr_scbond_other22.19814.2114565
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other33.65525.1416711
ELECTRON MICROSCOPYr_long_range_B_refined45.466291.24129469
ELECTRON MICROSCOPYr_long_range_B_other45.466291.24129470
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.21→3.293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.824 10743 -
obs--100 %

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