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

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Basic information

Entry
Database: PDB / ID: 9nqy
TitleNipah Virus Matrix Lattice in Complex with Human Cell Membrane
ComponentsMatrix protein
KeywordsVIRUS LIKE PARTICLE / Assembly Lattice
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
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 7 Å
AuthorsUpadhye, V.V. / Dick, R.A.
Funding support United States, 3items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Matrix protein
A: Matrix protein
B: Matrix protein
C: Matrix protein
E: Matrix protein
F: Matrix protein
G: Matrix protein
H: Matrix protein
I: Matrix protein
M: Matrix protein
J: Matrix protein
K: Matrix protein
L: Matrix protein
N: Matrix protein
O: Matrix protein
P: Matrix protein
Q: Matrix protein
R: Matrix protein


Theoretical massNumber of molelcules
Total (without water)802,06218
Polymers802,06218
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
Matrix protein / Protein M


Mass: 44558.980 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Henipavirus nipahense / Production host: Homo sapiens (human) / References: UniProt: Q9IK90
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Henipavirus nipahense / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Henipavirus nipahense / Strain: Malaysia
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: YES / Enveloped: YES / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
150 mMTris1
2150 mMNaCl1
31 mMEDTA1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 63000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 3.65 e/Å2 / Avg electron dose per subtomogram: 150 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 1
EM imaging opticsEnergyfilter name: GIF Bioquantum / Details: Zero Loss Peak was refined after every tilt series / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1Dynamo1.1.532volume selection
2SerialEM4.0.1image acquisition
4CTFFIND4CTF correction
7UCSF Chimera1.1.4model fitting
9PHENIX1.21_5207model refinement
11RELION4.0 Tomofinal Euler assignmentTomo
13RELION4.0 Tomo3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9767 / Symmetry type: POINT
EM volume selectionMethod: Manually annotated / Num. of tomograms: 24 / Num. of volumes extracted: 340688 / Reference model: Ab-initio
Atomic model buildingB value: 351 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: CC
Details: The 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. ...Details: The 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.
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: THROUGHOUT
Displacement parametersBiso max: 384.78 Å2 / Biso mean: 217.9891 Å2 / Biso min: 141.26 Å2

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