9NUF | pdb_00009nuf

Cryo-EM structure of the Nipah Virus nucleocapsid complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural insights into the Nipah virus nucleocapsid assembly.

Yang, G.Kompaniiets, D.Wang, D.Liu, B.

(2026) Commun Biol 

  • DOI: https://doi.org/10.1038/s42003-026-10379-6
  • Primary Citation Related Structures: 
    9NUF

  • PubMed 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 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.


  • Organizational Affiliation
    • Section of Transcription & Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN, USA.

Macromolecule Content 

  • Total Structure Weight: 840.92 kDa 
  • Atom Count: 44,996 
  • Modeled Residue Count: 5,656 
  • Deposited Residue Count: 7,532 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleoprotein532Henipavirus nipahenseMutation(s): 0 
UniProt
Find proteins for Q9IK92 (Nipah virus)
Explore Q9IK92 
Go to UniProtKB:  Q9IK92
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9IK92
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (84-MER)O [auth Z]84Henipavirus nipahense
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-25
    Type: Initial release
  • Version 1.1: 2026-06-10
    Changes: Data collection, Database references