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- EMDB-55587: Helical reconstruction of Langya henipavirus N-core nucleocapsid-... -

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Basic information

Entry
Database: EMDB / ID: EMD-55587
TitleHelical reconstruction of Langya henipavirus N-core nucleocapsid-like complex
Map dataHelical reconstruction of RNA-bound Langya virus N-core
Sample
  • Complex: Langya virus N-core
    • Protein or peptide: Nucleocapsid
    • RNA: RNA (5'-R(*AP*AP*AP*AP*AP*A)-3')
KeywordsHenipavirus / Langya virus / cryo-EM / nucleocapsid / nucleoprotein / RNA / VIRAL PROTEIN
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 / synthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsJayachandran RB / Quignon E / Renner M
Funding support Sweden, 1 items
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, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55587.png

Downloads & links

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Map

FileDownload / File: emd_55587.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical reconstruction of RNA-bound Langya virus N-core
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 400 pix.
= 368. Å		0.92 Å/pix.
x 400 pix.
= 368. Å		0.92 Å/pix.
x 400 pix.
= 368. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.30149722 - 0.628903
Average (Standard dev.)0.0053960127 (±0.039220784)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 368.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55587_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_55587_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_55587_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Langya virus N-core

EntireName: Langya virus N-core
Components
  • Complex: Langya virus N-core
    • Protein or peptide: Nucleocapsid
    • RNA: RNA (5'-R(*AP*AP*AP*AP*AP*A)-3')

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Supramolecule #1: Langya virus N-core

SupramoleculeName: Langya virus N-core / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Langya virus / Strain: Isolate SDQD_H1801

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Macromolecule #1: Nucleocapsid

MacromoleculeName: Nucleocapsid / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Langya virus / Strain: Isolate SDQD_H1801
Molecular weightTheoretical: 51.199469 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHGKP IPNPLLGLDS TENLYFQGID PFTMFSTLKN ETEKFREYQA NLGRQGKPLA STATLTTKII VYNPSNKSPA LRWEITKFA MRLIWSPAAS HSVKVGAALT LLSAHAENPG AMIRSLVNDP DIEVVITDIS EFDHGVPRLE RRGEKAEQQM D SYRRILDR ...String:
MHHHHHHGKP IPNPLLGLDS TENLYFQGID PFTMFSTLKN ETEKFREYQA NLGRQGKPLA STATLTTKII VYNPSNKSPA LRWEITKFA MRLIWSPAAS HSVKVGAALT LLSAHAENPG AMIRSLVNDP DIEVVITDIS EFDHGVPRLE RRGEKAEQQM D SYRRILDR APQENLFYNP EVDDLEILDS GTFLFAIATV LAQVWILVAK AVTAPDTAEE SENKRWAKYV QQKRVNPDYL VS NRWITAM RSLISIDLSV RKYMVEILIE VKKSGVARGR LNEMIADIGN YIEETGMAGF FLTIKYGLEM KFPVIVINEF QAD LLTLQT LMRTYMDLGP RAPYMVLLED SIQTKFAPGN YPLLWSFAMG VGTTLDRSMG ALNINRSYLE PIYFKLGQNA ARKN AGSID RKLAEELGLT QEQANEIKEM MQEVTTQRHE TNVQAREGKF NVAAGGIE

UniProtKB: Nucleocapsid

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Macromolecule #2: RNA (5'-R(*AP*AP*AP*AP*AP*A)-3')

MacromoleculeName: RNA (5'-R(*AP*AP*AP*AP*AP*A)-3') / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.930277 KDa
SequenceString:
AAAAAA

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.38 Å
Applied symmetry - Helical parameters - Δ&Phi: -27.86 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 170777
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9t5l:
Helical reconstruction of Langya henipavirus N-core nucleocapsid-like complex

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