4N8C | pdb_00004n8c

Three-dimensional structure of the extracellular domain of Matrix protein 2 of influenza A virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.242 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structure of the extracellular domain of matrix protein 2 of influenza A virus in complex with a protective monoclonal antibody

Cho, K.J.Schepens, B.Seok, J.H.Kim, S.Roose, K.Lee, J.H.Gallardo, R.Hamme, E.V.Schymkowitz, J.Rousseau, F.Fiers, W.Saelens, X.Kim, K.H.

(2015) J Virol 89: 3700-3711

  • DOI: https://doi.org/10.1128/JVI.02576-14
  • Primary Citation Related Structures: 
    4N8C

  • PubMed Abstract: 

    The extracellular domain of influenza A virus matrix protein 2 (M2e) is conserved and is being evaluated as a quasiuniversal influenza A vaccine candidate. We describe the crystal structure at 1.6 Å resolution of M2e in complex with the Fab fragment of an M2e-specific monoclonal antibody that protects against influenza A virus challenge. This antibody binds M2 expressed on the surfaces of cells infected with influenza A virus. Five out of six complementary determining regions interact with M2e, and three highly conserved M2e residues are critical for this interaction. In this complex, M2e adopts a compact U-shaped conformation stabilized in the center by the highly conserved tryptophan residue in M2e. This is the first description of the three-dimensional structure of M2e. M2e of influenza A is under investigation as a universal influenza A vaccine, but its three-dimensional structure is unknown. We describe the structure of M2e stabilized with an M2e-specific monoclonal antibody that recognizes natural M2. We found that the conserved tryptophan is positioned in the center of the U-shaped structure of M2e and stabilizes its conformation. The structure also explains why previously reported in vivo escape viruses, selected with a similar monoclonal antibody, carried proline residue substitutions at position 10 in M2.


  • Organizational Affiliation
    • Department of Biotechnology & Bioinformatics, College of Science & Technology, Korea University, Sejong, South Korea Inflammation Research Center, VIB, Ghent, Belgium Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.

Macromolecule Content 

  • Total Structure Weight: 101.82 kDa 
  • Atom Count: 7,783 
  • Modeled Residue Count: 909 
  • Deposited Residue Count: 928 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain of monoclonal antibodyA [auth H],
B [auth I]
221Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain of monoclonal antibodyC [auth L],
D [auth M]
220Mus musculusMutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Extracellular domain of influenza Matrix protein 2E [auth X],
F [auth Y]
23Influenza A virus (A/Puerto Rico/8/1934(H1N1))Mutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.242 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.353α = 86.88
b = 72.276β = 77.53
c = 78.446γ = 84.63
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2015-09-30
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Structure summary