2KQT

Solid-state NMR structure of the M2 transmembrane peptide of the influenza A virus in DMPC lipid bilayers bound to deuterated amantadine

Experimental Data Snapshot

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 24 
  • Conformers Submitted: 17 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2KAD 2H95


Literature

Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers

Cady, S.D., Schmidt-Rohr, K., Wang, J., Soto, C., DeGrado, W.F., Hong, M.

(2010) Nature 463: 689-692

  • DOI: 10.1038/nature08722
  • Primary Citation of Related Structures:  
    2KQT

  • PubMed Abstract: 

    • The M2 protein of influenza A virus is a membrane-spanning tetrameric proton channel targeted by the antiviral drugs amantadine and rimantadine. Resistance to these drugs has compromised their effectiveness against many influenza strains, including pandemic H1N1 ...

    The M2 protein of influenza A virus is a membrane-spanning tetrameric proton channel targeted by the antiviral drugs amantadine and rimantadine. Resistance to these drugs has compromised their effectiveness against many influenza strains, including pandemic H1N1. A recent crystal structure of M2(22-46) showed electron densities attributed to a single amantadine in the amino-terminal half of the pore, indicating a physical occlusion mechanism for inhibition. However, a solution NMR structure of M2(18-60) showed four rimantadines bound to the carboxy-terminal lipid-facing surface of the helices, suggesting an allosteric mechanism. Here we show by solid-state NMR spectroscopy that two amantadine-binding sites exist in M2 in phospholipid bilayers. The high-affinity site, occupied by a single amantadine, is located in the N-terminal channel lumen, surrounded by residues mutated in amantadine-resistant viruses. Quantification of the protein-amantadine distances resulted in a 0.3 A-resolution structure of the high-affinity binding site. The second, low-affinity, site was observed on the C-terminal protein surface, but only when the drug reaches high concentrations in the bilayer. The orientation and dynamics of the drug are distinct in the two sites, as shown by (2)H NMR. These results indicate that amantadine physically occludes the M2 channel, thus paving the way for developing new antiviral drugs against influenza viruses. The study demonstrates the ability of solid-state NMR to elucidate small-molecule interactions with membrane proteins and determine high-resolution structures of their complexes.

    Related Citations: 
    • Structure of amantadine-bound M2 transmembrane peptide of influenza A in lipid bilayers from magic-angle-spinning solid-state NMR: the role of Ser31 in amantadine binding.
      Cady, S.D., Mishanina, T.V., Hong, M.
      (2009) J Mol Biol 385: 1127
    • Backbone structure of the amantadine-blocked trans-membrane domain M2 proton channel from Influenza A virus.
      Hu, J., Asbury, T., Achuthan, S., Li, C., Bertram, R., Quine, J.R., Fu, R., Cross, T.A.
      (2007) Biophys J 92: 4335
    Organizational Affiliation: 

    Department of Chemistry, Iowa State University, Ames, Iowa 50011 2, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
M2 proteinA, B, C, D25N/AMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O70632 (Influenza A virus (strain A/Hong Kong/156/1997 H5N1 genotype Gs/Gd))
Explore O70632 
Go to UniProtKB:  O70632
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO70632
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
308
Query on 308
Download Ideal Coordinates CCD File 
E [auth C](3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine
C10 H17 N
DKNWSYNQZKUICI-CHIWXEEVSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 24 
  • Conformers Submitted: 17 
  • Selection Criteria: structures with the least restraint violations 
  • OLDERADO: 2KQT Olderado

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-10-26
    Changes: Other
  • Version 1.3: 2020-02-26
    Changes: Data collection, Database references, Other