4QKM

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1073/pnas.1518493112
  • Structures With Same Primary Citation

  • 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 st ...

    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: 

    Department of Pharmaceutical Chemistry, University of San Francisco, San Francisco, CA 94158; william.degrado@ucsf.edu giacomo.fiorin@temple.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
influenza M2 monomer
A
27Influenza A virus (A/udorn/1972(H3N2))Mutation(s): 2 
Find proteins for P0DOF5 (Influenza A virus (strain A/Udorn/307/1972 H3N2))
Go to UniProtKB:  P0DOF5
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLB
Query on OLB
Download CCD File 
A
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-QJRAZLAKSA-N		 Ligand Interaction
EDO
Query on EDO
Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.151 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.09α = 90
b = 30.09β = 90
c = 67.39γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references