4N8C

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 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

Starting Model: experimental
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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 of 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of monoclonal antibodyA [auth H],
B [auth I]
221Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of monoclonal antibodyC [auth L],
D [auth M]
220Mus musculusMutation(s): 0 
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  • Reference Sequence

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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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • 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

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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