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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: Commun Biol / Year: 2026
Title: Structural insights into the Nipah virus nucleocapsid assembly.
Authors: Ge Yang / Dmytro Kompaniiets / Dong Wang / Bin Liu /
Abstract: Nipah virus (NiV), a lethal zoonotic henipavirus, poses a major public health threat. Its nucleoprotein (N) safeguards the genome by forming a nucleocapsid, which, together with the RNA-dependent RNA ...Nipah virus (NiV), a lethal zoonotic henipavirus, poses a major public health threat. Its nucleoprotein (N) safeguards the genome by forming a nucleocapsid, which, together with the RNA-dependent RNA polymerase (L) and phosphoprotein (P), constitutes the ribonucleoprotein complex. Here, we report a 2.96 Å cryo-EM structure of the NiV nucleocapsid co-expressed with L and P. The structure, resolved under C1 symmetry without imposing helical or other symmetry restraints, reveals irregular helical packing and axis bending that likely reflect the physiological nucleocapsid. Detailed analysis defines N-N and N-RNA interfaces, including critical salt bridges and hydrogen bonds, and uncovers a previously unrecognized loop-mediated contact bridging adjacent turns. Functional validation by site-directed mutagenesis and minigenome assays establishes their potential role of these interactions in nucleocapsid stability. Collectively, these integrated structural and functional insights refine our understanding of NiV nucleocapsid assembly and highlight structural vulnerabilities that could be targeted for antiviral development.
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
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Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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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