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- PDB-9nuf: Cryo-EM structure of the Nipah Virus nucleocapsid complex -

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Basic information

Entry
Database: PDB / ID: 9nuf
TitleCryo-EM structure of the Nipah Virus nucleocapsid complex
Components
  • Nucleoprotein
  • RNA (84-MER)
KeywordsVIRAL PROTEIN/RNA / Nipah virus / nucleocapsid (N) protein / ribonucleoprotein (RNP) complex / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


negative stranded viral RNA transcription / negative stranded viral RNA replication / helical viral capsid / viral nucleocapsid / molecular adaptor activity / host cell cytoplasm / ribonucleoprotein complex / structural molecule activity / RNA binding
Similarity search - Function
Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein
Similarity search - Domain/homology
RNA / RNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesHenipavirus nipahense
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsLiu, B. / Yang, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of the Nipah Virus nucleocapsid complex
Authors: Liu, B. / Yang, G.
History
DepositionMar 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 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

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Assembly

Deposited unit
D: Nucleoprotein
E: Nucleoprotein
F: Nucleoprotein
G: Nucleoprotein
H: Nucleoprotein
I: Nucleoprotein
J: Nucleoprotein
K: Nucleoprotein
L: Nucleoprotein
M: Nucleoprotein
N: Nucleoprotein
O: Nucleoprotein
P: Nucleoprotein
Q: Nucleoprotein
Z: RNA (84-MER)


Theoretical massNumber of molelcules
Total (without water)840,92015
Polymers840,92015
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Nucleoprotein / Protein N / Nucleocapsid protein


Mass: 58231.898 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Henipavirus nipahense / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9IK92
#2: RNA chain RNA (84-MER)


Mass: 25672.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Henipavirus nipahense
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: The Nipah Virus nucleocapsid complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.01 MDa / Experimental value: NO
Source (natural)Organism: Henipavirus nipahense
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 77 K / Temperature (min): 63 K
Image recordingAverage exposure time: 1.7 sec. / Electron dose: 50.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6267
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21_5207model refinement
3EPUimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1326637
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 138389 / Symmetry type: POINT
Atomic model buildingB value: 55.4 / Protocol: OTHER / Space: REAL
RefinementHighest resolution: 2.96 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00445905
ELECTRON MICROSCOPYf_angle_d0.87262380
ELECTRON MICROSCOPYf_dihedral_angle_d6.6997123
ELECTRON MICROSCOPYf_chiral_restr0.0517210
ELECTRON MICROSCOPYf_plane_restr0.0097728

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