9T5K | pdb_00009t5k

Local refinement of RNA-free assembled Langya virus N-core

• PDB DOI: https://doi.org/10.2210/pdb9T5K/pdb
• EM Map EMD-55586: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Langya virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-11-05 Released: 2026-04-22 
• Deposition Author(s): Jayachandran, R.B., Quignon, E., Renner, M.
• Funding Organization(s): Kempe Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Open and closed forms of assembled henipavirus nucleoprotein suggest structural basis of genome access.

Jayachandran, R.B., Quignon, E., Renner, M.

(2026) Sci Adv 12: eaed8300-eaed8300

• PubMed: 42127178 
• DOI: https://doi.org/10.1126/sciadv.aed8300
• Primary Citation Related Structures: 
  9T5K, 9T5L


• PubMed Abstract: 
  

  Henipaviruses, such as Nipah virus, can cause deadly illness and constitute WHO blueprint priorities due to their pandemic potential. Their genomes are packaged within a nucleocapsid consisting of viral nucleoproteins (N). Now, it is unclear how the encapsidated genome is released from N to allow the viral polymerase to read its sequence. Here, we present the high-resolution cryo-EM structure of a helical N-RNA filament from Langya henipavirus (LayV), allowing us to identify vertical interactions crucial for assembly. We show that assembly efficiency is sequence-dependent and prefers 5'-genomic sequences. Further, we solve the structure of an RNA-free assembly of LayV-N. Structural comparison of the RNA-bound and RNA-free LayV-N shows a conformational opening and closing, even within the assembled state. Our data suggest that N within nucleocapsids may undergo local conformational changes, switching between closed and open states, to temporarily allow access to the encapsidated RNA without nucleocapsid disruption.

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Organizational Affiliation: 
• Department of Chemistry, Umeå University, 901 87 Umeå, Sweden.
Umeå Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden.
Department of Clinical Microbiology, Umeå University, 901 87 Umeå, Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 51.2 kDa 
• Atom Count: 3,030 
• Modeled Residue Count: 381 
• Deposited Residue Count: 453 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleocapsid	A	453	Langya virus	Mutation(s): 0
UniProt
Find proteins for A0AAX3C958 (Langya virus) Explore A0AAX3C958  Go to UniProtKB:  A0AAX3C958

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.5.3
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-22 
Deposition Author(s): Jayachandran, R.B., Quignon, E., Renner, M.

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Funding Organization	Location	Grant Number
Kempe Foundation	Sweden	JCK 23135

Revision History  

• Version 1.0: 2026-04-22
  Type: Initial release
  
• Version 1.1: 2026-05-27
  Changes: Data collection, Database references