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- PDB-9t5k: Local refinement of RNA-free assembled Langya virus N-core -

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Basic information

Entry
Database: PDB / ID: 9t5k
TitleLocal refinement of RNA-free assembled Langya virus N-core
ComponentsNucleocapsid
KeywordsVIRAL PROTEIN / Henipavirus / Langya virus / cryo-EM / nucleocapsid / nucleoprotein / RNA
Function / homologyParamyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / structural molecule activity / RNA binding / Nucleocapsid
Function and homology information
Biological speciesLangya virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsJayachandran, R.B. / Quignon, E. / Renner, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Kempe FoundationJCK 23135 Sweden
CitationJournal: Sci Adv / Year: 2026
Title: Open and closed forms of assembled henipavirus nucleoprotein suggest structural basis of genome access.
Authors: Rupesh Balaji Jayachandran / Erwan Quignon / Max Renner /
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 ...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.
History
DepositionNov 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleocapsid


Theoretical massNumber of molelcules
Total (without water)51,1991
Polymers51,1991
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Nucleocapsid / Nucleocapsid protein


Mass: 51199.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Langya virus / Strain: Isolate SDQD_H1801 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAX3C958
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: Langya virus N-core / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Langya virus / Strain: Isolate SDQD_H1801
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
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 R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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 defocus max: 2400 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
4cryoSPARC4.5.3CTF correction
9cryoSPARC4.5.3initial Euler assignment
10cryoSPARC4.5.3final Euler assignment
11cryoSPARC4.5.3classification
12cryoSPARC4.5.33D reconstruction
13PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7037732 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 2.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0023085
ELECTRON MICROSCOPYf_angle_d0.3914174
ELECTRON MICROSCOPYf_dihedral_angle_d3.334413
ELECTRON MICROSCOPYf_chiral_restr0.037477
ELECTRON MICROSCOPYf_plane_restr0.003531

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