5TTC

XFEL structure of influenza A M2 wild type TM domain at high pH in the lipidic cubic phase at room temperature


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction.

Thomaston, J.L.Woldeyes, R.A.Nakane, T.Yamashita, A.Tanaka, T.Koiwai, K.Brewster, A.S.Barad, B.A.Chen, Y.Lemmin, T.Uervirojnangkoorn, M.Arima, T.Kobayashi, J.Masuda, T.Suzuki, M.Sugahara, M.Sauter, N.K.Tanaka, R.Nureki, O.Tono, K.Joti, Y.Nango, E.Iwata, S.Yumoto, F.Fraser, J.S.DeGrado, W.F.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 13357-13362

  • DOI: 10.1073/pnas.1705624114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The M2 proton channel of influenza A is a drug target that is essential for the reproduction of the flu virus. It is also a model system for the study of selective, unidirectional proton transport across a membrane. Ordered water molecules arranged i ...

    The M2 proton channel of influenza A is a drug target that is essential for the reproduction of the flu virus. It is also a model system for the study of selective, unidirectional proton transport across a membrane. Ordered water molecules arranged in "wires" inside the channel pore have been proposed to play a role in both the conduction of protons to the four gating His37 residues and the stabilization of multiple positive charges within the channel. To visualize the solvent in the pore of the channel at room temperature while minimizing the effects of radiation damage, data were collected to a resolution of 1.4 Å using an X-ray free-electron laser (XFEL) at three different pH conditions: pH 5.5, pH 6.5, and pH 8.0. Data were collected on the Inwardopen state, which is an intermediate that accumulates at high protonation of the His37 tetrad. At pH 5.5, a continuous hydrogen-bonded network of water molecules spans the vertical length of the channel, consistent with a Grotthuss mechanism model for proton transport to the His37 tetrad. This ordered solvent at pH 5.5 could act to stabilize the positive charges that build up on the gating His37 tetrad during the proton conduction cycle. The number of ordered pore waters decreases at pH 6.5 and 8.0, where the Inwardopen state is less stable. These studies provide a graphical view of the response of water to a change in charge within a restricted channel environment.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Matrix protein 2
A
27Influenza A virus (strain A/Hickox/1940 H1N1)Gene Names: M (M2)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
M2 proton channel (AM2)
Find proteins for Q0HD59 (Influenza A virus (strain A/Hickox/1940 H1N1))
Go to UniProtKB:  Q0HD59
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
A
NON-POLYMERH2 N

--

ACE
Query on ACE
A
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 29.826α = 90.00
b = 29.826β = 90.00
c = 68.011γ = 90.00
Software Package:
Software NamePurpose
cctbx.primedata scaling
PHENIXrefinement
cctbx.xfeldata reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01-GM056423

Revision History 

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Data collection, Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence
  • Version 1.3: 2018-01-03
    Type: Database references