7SKS | pdb_00007sks

Crystal structure of measles virus matrix protein

• PDB DOI: https://doi.org/10.2210/pdb7SKS/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Measles virus strain Ichinose-B95a
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2021-10-21 Released: 2022-08-24 
• Deposition Author(s): Norris, M.J., Saphire, E.O.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 
  0.257 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Measles and Nipah virus assembly: Specific lipid binding drives matrix polymerization.

Norris, M.J., Husby, M.L., Kiosses, W.B., Yin, J., Saxena, R., Rennick, L.J., Heiner, A., Harkins, S.S., Pokhrel, R., Schendel, S.L., Hastie, K.M., Landeras-Bueno, S., Salie, Z.L., Lee, B., Chapagain, P.P., Maisner, A., Duprex, W.P., Stahelin, R.V., Saphire, E.O.

(2022) Sci Adv 8: eabn1440-eabn1440

• PubMed: 35857835 
• DOI: https://doi.org/10.1126/sciadv.abn1440
• Primary Citation Related Structures: 
  7SKS, 7SKT, 7SKU


• PubMed Abstract: 
  

  Measles virus, Nipah virus, and multiple other paramyxoviruses cause disease outbreaks in humans and animals worldwide. The paramyxovirus matrix (M) protein mediates virion assembly and budding from host cell membranes. M is thus a key target for antivirals, but few high-resolution structures of paramyxovirus M are available, and we lack the clear understanding of how viral M proteins interact with membrane lipids to mediate viral assembly and egress that is needed to guide antiviral design. Here, we reveal that M proteins associate with phosphatidylserine and phosphatidylinositol 4,5-bisphosphate [PI(4,5)P ₂ ] at the plasma membrane. Using x-ray crystallography, electron microscopy, and molecular dynamics, we demonstrate that PI(4,5)P ₂ binding induces conformational and electrostatic changes in the M protein surface that trigger membrane deformation, matrix layer polymerization, and virion assembly.

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Organizational Affiliation: 
• Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA.
Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
Institute of Virology, Philipps University Marburg, Marburg, Germany.
Department of Physics, Florida International University, Miami, FL 33199, USA.
Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering, electron microscopy, microscopy

Macromolecule Content 

• Total Structure Weight: 83.47 kDa 
• Atom Count: 4,484 
• Modeled Residue Count: 553 
• Deposited Residue Count: 752 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrix protein	A, B	376	Measles virus strain Ichinose-B95a	Mutation(s): 0  Gene Names: M
UniProt
Find proteins for Q9W850 (Measles virus (strain Ichinose-B95a)) Explore Q9W850  Go to UniProtKB:  Q9W850

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free:  0.257 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.954	α = 90
b = 85.954	β = 90
c = 402.506	γ = 120

Software Package:

Software Name	Purpose
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
TRUNCATE	data processing
BUSTER	refinement
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-24 
Deposition Author(s): Norris, M.J., Saphire, E.O.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2022-08-24
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description