6OUG

Structure of drug-resistant V27A mutant of the influenza M2 proton channel bound to spiroadamantyl amine inhibitor, TM + cytosolic helix construct


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.273 

wwPDB Validation 3D Report Full Report


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Literature

X-ray crystal structures of the influenza M2 proton channel drug-resistant V27A mutant bound to a spiro-adamantyl amine inhibitor reveal the mechanism of adamantane resistance.

Thomaston, J.L.Konstantinidi, A.Liu, L.Lambrinidis, G.Tan, J.Caffrey, M.Wang, J.Degrado, W.F.Kolocouris, A.

(2020) Biochemistry --: --

  • DOI: 10.1021/acs.biochem.9b00971
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The V27A mutation confers adamantane resistance on the influenza A matrix 2 (M2) proton channel and is becoming more prevalent in circulating populations of influenza A virus. We have used X-ray crystallography to determine structures of a spiro-adam ...

    The V27A mutation confers adamantane resistance on the influenza A matrix 2 (M2) proton channel and is becoming more prevalent in circulating populations of influenza A virus. We have used X-ray crystallography to determine structures of a spiro-adamantyl amine inhibitor bound to M2(22-46) V27A and also to M2(21-61) V27A in the Inward closed conformation. The spiro-adamantyl amine binding site is nearly identical for the two crystal structures. Compared to the M2 "wild type" (WT) with valine at position 27, we observe that the channel pore is wider at its N-terminus as a result of the V27A mutation and that this removes V27 side chain hydrophobic interactions that are important for binding of amantadine and rimantadine. The spiro-adamantyl amine inhibitor blocks proton conductance in the WT and V27A mutant channels by shifting its binding site in the pore depending on which residue is present at position 27. Additionally, in the structure of the M2(21-61) V27A construct, the C-terminus of the channel is tightly packed relative to that of the M2(22-46) construct. We observe that residues Asp44, Arg45, and Phe48 face the center of the channel pore and would be well-positioned to interact with protons exiting the M2 channel after passing through the His37 gate. A 300 ns molecular dynamics simulation of the M2(22-46) V27A-spiro-adamantyl amine complex predicts with accuracy the position of the ligands and waters inside the pore in the X-ray crystal structure of the M2(22-46) V27A complex.


    Organizational Affiliation

    State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen 518055 , China.,Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology , Trinity College Dublin , Dublin D02 R590 , Ireland.,Department of Pharmacology and Toxicology, College of Pharmacy , University of Arizona , Tucson , Arizona 85721 , United States.,Department of Pharmaceutical Chemistry , University of California San Francisco , San Francisco , California 94158 , United States.,DLX Scientific , Lawrence , Kansas 66049 , United States.,Department of Pharmaceutical Chemistry , National and Kapodistrian University of Athens , 15771 Athens , Greece.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Matrix protein 2
A, B, C, D, E, F, G, H
41Influenza A virus (strain A/Memphis/1/1971 H3N2)Mutation(s): 2 
Gene Names: M
Find proteins for Q3YPZ4 (Influenza A virus (strain A/Memphis/1/1971 H3N2))
Go to UniProtKB:  Q3YPZ4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E01
Query on E01

Download SDF File 
Download CCD File 
D, E
(1r,1'S,3'S,5'S,7'S)-spiro[cyclohexane-1,2'-tricyclo[3.3.1.1~3,7~]decan]-4-amine
C15 H25 N
VNTMIVFMVGTSHV-RLUXGHLOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.273 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 49.420α = 90.00
b = 49.380β = 90.00
c = 122.380γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR35-GM122603

Revision History 

  • Version 1.0: 2020-01-15
    Type: Initial release