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 

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.USA 112: 14260-14265

  • DOI: 10.1073/pnas.1518493112
  • Primary Citation of Related Structures:  

  • 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;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
influenza M2 monomer
A
27Influenza A virus (strain A/Udorn/307/1972 H3N2)Mutation(s): 0 
Gene Names: M
Find proteins for P0DOF5 (Influenza A virus (strain A/Udorn/307/1972 H3N2))
Go to UniProtKB:  P0DOF5
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLB
Query on OLB
Download SDF File 
Download CCD File 
A
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-QJRAZLAKSA-N
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA
Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO
Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
A
NON-POLYMERH2 N

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ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.148 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 30.090α = 90.00
b = 30.090β = 90.00
c = 67.390γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
MOSFLMdata reduction
Aimlessdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


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
    Type: Database references