Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.07 kDa 
• Atom Count: 779 
• Residue Count: 100 
• Unique protein chains: 1

2KQT

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

• DOI: 10.2210/pdb2KQT/pdb
• BMRB: 16612

• Classification: TRANSPORT PROTEIN
• Mutation(s): No 


• Deposited: 2009-11-18 Released: 2010-02-09 
• Deposition Author(s): Cady, S.D., Schmidt-Rohr, K., Wang, J., Soto, C.S., DeGrado, W.F., Hong, M.

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Experimental Data Snapshot

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

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

• PubMed: 20130653 
• 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. 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
M2 protein	A, B, C, D	25	N/A	Mutation(s): 0
Find proteins for O70632 (Influenza A virus (strain A/Hong Kong/156/1997 H5N1 genotype Gs/Gd)) Explore O70632  Go to UniProtKB:  O70632

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
308	C	(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine C10 H17 N DKNWSYNQZKUICI-CHIWXEEVSA-N

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

Entry History 

Deposition Data

• Deposited Date: 2009-11-18 
• Released Date: 2010-02-09 
Deposition Author(s): Cady, S.D., Schmidt-Rohr, K., Wang, J., Soto, C.S., DeGrado, W.F., Hong, M.

Revision History 

• 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