9NQY | pdb_00009nqy

Nipah Virus Matrix Lattice in Complex with Human Cell Membrane

• PDB DOI: https://doi.org/10.2210/pdb9NQY/pdb
• EM Map EMD-49696: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Henipavirus nipahense
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-03-13 Released: 2026-08-19 
• Deposition Author(s): Upadhye, V.V., Dick, R.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 7.00 Å
• Aggregation State: 3D ARRAY 
• Reconstruction Method: SUBTOMOGRAM AVERAGING 

Starting Model: in silico

Literature

Cryo-electron tomography of Nipah virus structural protein complexes in virus-like particles.

Upadhye, V.V., Lee, J.F., Ercanli, N., Ricana, C., Hinsley, A.C., Obr, M., Autin, L., Schur, F.K.M., Aguilar, H.C., Dick, R.A.

(2026) bioRxiv 

• PubMed: 42523209 
• DOI: https://doi.org/10.64898/2026.07.16.738223
• Primary Citation Related Structures: 
  9NQY


• PubMed 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, 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.

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Organizational Affiliation: 
• Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY.
Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA.
Center for ViroScience and Cure, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA.
Material and Structural Analysis Division, Thermo Fisher Scientific, Eindhoven, Netherlands.
Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 18-mer - A18 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 802.06 kDa 
• Atom Count: 30,060 
• Modeled Residue Count: 6,102 
• Deposited Residue Count: 7,038 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrix protein	A [auth D], B [auth A], C [auth B], D [auth C], E, F, G, H, I, J [auth M], K [auth J], L [auth K], M [auth L], N, O, P, Q, R	391	Henipavirus nipahense	Mutation(s): 0
UniProt
Find proteins for Q9IK90 (Nipah virus) Explore Q9IK90  Go to UniProtKB:  Q9IK90

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 7.00 Å
• Aggregation State: 3D ARRAY 
• Reconstruction Method: SUBTOMOGRAM AVERAGING 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207
RECONSTRUCTION	RELION	4.0 Tomo

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-08-19 
Deposition Author(s): Upadhye, V.V., Dick, R.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI109022
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI147890-04
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI150479-09

Revision History  

• Version 1.0: 2026-08-19
  Type: Initial release