9NUF

Cryo-EM structure of the Nipah Virus nucleocapsid complex

Summary for 9NUF

• Entry DOI: 10.2210/pdb9nuf/pdb
• EMDB information: 49803
• Descriptor: Nucleoprotein, RNA (84-MER) (2 entities in total)
• Functional Keywords: nipah virus, nucleocapsid (n) protein, ribonucleoprotein (rnp) complex, viral protein-rna complex, viral protein/rna
• Biological source: Henipavirus nipahense; More
• Total number of polymer chains: 15
• Total formula weight: 840919.56

Authors

Liu, B.,Yang, G. (deposition date: 2025-03-19, release date: 2026-03-25, Last modification date: 2026-06-10)

Primary citation

Yang, G.,Kompaniiets, D.,Wang, D.,Liu, B.
Structural insights into the Nipah virus nucleocapsid assembly.
Commun Biol, 2026

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.

PubMed: 42204270
DOI: 10.1038/s42003-026-10379-6

Experimental method

ELECTRON MICROSCOPY (2.96 Å)