4QKC

Influenza A M2 wild type TM domain at low pH in the lipidic cubic phase under cryo diffraction conditions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.128 
  • R-Value Work: 0.108 
  • R-Value Observed: 0.110 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction.

Thomaston, J.L.Alfonso-Prieto, M.Woldeyes, R.A.Fraser, J.S.Klein, M.L.Fiorin, G.DeGrado, W.F.

(2015) Proc Natl Acad Sci U S A 112: 14260-14265

  • DOI: https://doi.org/10.1073/pnas.1518493112
  • Primary Citation of Related Structures:  
    4QK7, 4QKC, 4QKL, 4QKM

  • PubMed Abstract: 

    The matrix 2 (M2) protein from influenza A virus is a proton channel that uses His37 as a selectivity filter. Here we report high-resolution (1.10 Å) cryogenic crystallographic structures of the transmembrane domain of M2 at low and high pH. These structures reveal that waters within the pore form hydrogen-bonded networks or "water wires" spanning 17 Å from the channel entrance to His37. Pore-lining carbonyl groups are well situated to stabilize hydronium via second-shell interactions involving bridging water molecules. In addition, room temperature crystallographic structures indicate that water becomes increasingly fluid with increasing temperature and decreasing pH, despite the higher electrostatic field. Complementary molecular dynamics simulations reveal a collective switch of hydrogen bond orientations that can contribute to the directionality of proton flux as His37 is dynamically protonated and deprotonated in the conduction cycle.


  • Organizational Affiliation

    Institute of Computational Molecular Science, Temple University, Philadelphia, PA 19122;


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
influenza M2 monomer27Influenza A virus (A/udorn/1972(H3N2))Mutation(s): 2 
Membrane Entity: Yes 
UniProt
Find proteins for P0DOF5 (Influenza A virus (strain A/Udorn/307/1972 H3N2))
Explore P0DOF5 
Go to UniProtKB:  P0DOF5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DOF5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.128 
  • R-Value Work: 0.108 
  • R-Value Observed: 0.110 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.31α = 90
b = 29.31β = 90
c = 67.31γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description