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- EMDB-49696: Subtomogram Average of the Nipah Virus Matrix Lattice in Complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-49696
TitleSubtomogram Average of the Nipah Virus Matrix Lattice in Complex with Human Cell Membrane inside Virus-Like-Particles
Map data
Sample
  • Virus: Henipavirus nipahense
    • Protein or peptide: Matrix protein
KeywordsAssembly Lattice / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


virion assembly / virion component / structural constituent of virion / host cell cytoplasm / host cell nucleus / host cell plasma membrane
Similarity search - Function
: / Paramyxoviridae matrix protein C-terminal domain / Viral matrix protein / Viral matrix protein, C-terminal domain / Viral matrix protein, N-terminal domain / Paramyxoviridae matrix protein N-terminal domain
Similarity search - Domain/homology
Biological speciesHenipavirus nipahense
Methodsubtomogram averaging / cryo EM / Resolution: 7.0 Å
AuthorsUpadhye VV / Dick RA
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI109022 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI147890-04 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI150479-09 United States
CitationJournal: bioRxiv / Year: 2026
Title: Cryo-electron tomography of Nipah virus structural protein complexes in virus-like particles.
Authors: Viraj V Upadhye / Jean F Lee / Nihan Ercanli / Clifton Ricana / Amy C Hinsley / Martin Obr / Ludovic Autin / Florian K M Schur / Hector C Aguilar / Robert A Dick /
Abstract: Nipah virus (NiV) is a BSL-4 zoonotic paramyxovirus with ~75% human mortality. The matrix protein (M) of NiV and other paramyxoviruses binds the inner leaflet of the cellular plasma membrane, ...Nipah virus (NiV) is a BSL-4 zoonotic paramyxovirus with ~75% human mortality. The matrix protein (M) of NiV and other paramyxoviruses binds the inner leaflet of the cellular plasma membrane, orchestrating virion assembly by bringing together transmembrane glycoproteins (F/G) and ribonucleoprotein complexes (N). However, the interactions of these full-length proteins within membrane complexes remain elusive. Using cryo-electron tomography and subtomogram averaging of virus like particles (VLPs), we interrogated the protein:protein interactions of the main NiV structural proteins M/N/F/G. The M lattice structure determined to 7Å revealed a novel M-dimer arrangement that yielded two distinct repeating holes. Notably, F-trimers were arranged above only one of the two holes, dependent on F's cytoplasmic tail. G was enriched in regions of higher M-VLP curvature, while N dramatically increased M-VLP pleomorphism. This work provides novel insights into paramyxoviral protein complexes, structures, and morphology.
History
DepositionMar 13, 2025-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49696.png

Downloads & links

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Map

FileDownload / File: emd_49696.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 260 pix.
= 340.6 Å		1.31 Å/pix.
x 260 pix.
= 340.6 Å		1.31 Å/pix.
x 260 pix.
= 340.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.8
Minimum - Maximum-14.846776999999999 - 19.354372000000001
Average (Standard dev.)0.000010302783 (±0.7783937)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 340.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49696_msk_1.map
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Additional map: merged unfiltered map

Fileemd_49696_additional_1.map
Annotationmerged unfiltered map
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Half map: #2

Fileemd_49696_half_map_1.map
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Half map: #1

Fileemd_49696_half_map_2.map
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Sample components

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Entire : Henipavirus nipahense

EntireName: Henipavirus nipahense
Components
  • Virus: Henipavirus nipahense
    • Protein or peptide: Matrix protein

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Supramolecule #1: Henipavirus nipahense

SupramoleculeName: Henipavirus nipahense / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 3052225 / Sci species name: Henipavirus nipahense / Sci species strain: Malaysia / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: Yes

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Macromolecule #1: Matrix protein

MacromoleculeName: Matrix protein / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 44.55898 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKD YKDDDDKDYK DDDDKARAGS PGLQEFDIKL EPDIKSISSE SMEGVSDFSP SSWEHGGYLD KVEPEIDENG SMIPKYKIY TPGANERKYN NYMYLICYGF VEDVERTPET GKRKKIRTIA AYPLGVGKSA SHPQDLLEEL CSLKVTVRRT A GSTEKIVF ...String:
MDYKDDDDKD YKDDDDKDYK DDDDKARAGS PGLQEFDIKL EPDIKSISSE SMEGVSDFSP SSWEHGGYLD KVEPEIDENG SMIPKYKIY TPGANERKYN NYMYLICYGF VEDVERTPET GKRKKIRTIA AYPLGVGKSA SHPQDLLEEL CSLKVTVRRT A GSTEKIVF GSSGPLNHLV PWKKVLTSGS IFNAVKVCRN VDQIQLDKHQ ALRIFFLSIT KLNDSGIYMI PRTMLEFRRN NA IAFNLLV YLKIDADLSK MGIQGSLDKD GFKVASFMLH LGNFVRRAGK YYSVDYCRRK IDRMKLQFSL GSIGGLSLHI KIN GVISKR LFAQMGFQKN LCFSLMDINP WLNRLTWNNS CEISRVAAVL QPSIPREFMI YDDVFIDNTG RILKG

UniProtKB: Matrix protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state3D array

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationName
50.0 mMTris
150.0 mMNaCl
1.0 mMEDTA
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV / Details: Zero Loss Peak was refined after every tilt series
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 1 / Average electron dose: 3.65 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 63000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0 Tomo) / Number subtomograms used: 9767
ExtractionNumber tomograms: 24 / Number images used: 340688 / Reference model: Ab-initio / Method: Manually annotated / Software - Name: Dynamo (ver. 1.1.532)
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0 Tomo) / Software - details: Tomo
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsThe initial model of 1 M Dimer was generated with AlphaFold2. Model was docked into map in Chimera v1.1.4. RealSpaceRefine in Phenix of 1 M Dimer. Open refined model and map in Chimera. Duplicate model, rotate and dock. Re run RealSpaceRefine. Repeat for all dimers present in electron density map. Run comprehensive validation in Phenix which resulted in Ramachandran outliers of 0%, Allowed 7% and Favored of 93% . We then removed all side chains from model prior to PDB deposition since our map does not support any side chain density - only backbone.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 351 / Target criteria: CC
Output model

PDB-9nqy:
Nipah Virus Matrix Lattice in Complex with Human Cell Membrane

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