Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 2.87 kDa 
• Atom Count: 220 
• Modelled Residue Count: 27 
• Deposited Residue Count: 27 
• Unique protein chains: 1

 5UM1

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

• PDB DOI:  https://doi.org/10.2210/pdb5UM1/pdb

• Classification: PROTON TRANSPORT
• Organism(s): Influenza A virus (A/Hickox/1940(H1N1))
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMMemProtMDmpstruc


• Deposited: 2017-01-25 Released: 2017-08-23 
• Deposition Author(s): Thomaston, J.L., Woldeyes, R.A., Fraser, J.S., DeGrado, W.F.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.230 
• R-Value Work: 0.213 
• R-Value Observed: 0.214 

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

• PubMed: 28835537 
• DOI: https://doi.org/10.1073/pnas.1705624114
• Primary Citation of Related Structures:  
  5JOO, 5TTC, 5UM1


• 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 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 Inward _open 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 Inward _open 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.

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Organizational Affiliation: 

Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158; [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrix protein 2	A	27	Influenza A virus (A/Hickox/1940(H1N1))	Mutation(s): 2  Gene Names: M, M2 Membrane Entity: Yes
UniProt
Find proteins for Q0HD59 (Influenza A virus (strain A/Hickox/1940 H1N1)) Explore Q0HD59  Go to UniProtKB:  Q0HD59

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.230 
• R-Value Work: 0.213 
• R-Value Observed: 0.214 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.884	α = 90
b = 29.884	β = 90
c = 67.795	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
cctbx.xfel	data reduction
cctbx.prime	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-08-23 
Deposition Author(s): Thomaston, J.L., Woldeyes, R.A., Fraser, J.S., DeGrado, W.F.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM056423

Revision History  

• Version 1.0: 2017-08-23
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Data collection, Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence
• Version 1.3: 2018-01-03
  Changes: Database references
• Version 1.4: 2020-01-01
  Changes: Author supporting evidence