Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

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: 3.29 kDa 
• Atom Count: 323 
• Modelled Residue Count: 27 
• Deposited Residue Count: 27 
• Unique protein chains: 1

4QKM

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

• PDB DOI: 10.2210/pdb4QKM/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/udorn/1972(H3N2))
• Mutation(s): Yes 
• Membrane Protein: Yes  OPM


• Deposited: 2014-06-06 Released: 2015-11-11 
• Deposition Author(s): Thomaston, J.L., DeGrado, W.F.

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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 

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

• PubMed: 26578770 
• DOI: 10.1073/pnas.1518493112
• Primary Citation of Related Structures:  
  4QK7, 4QKC, 4QKL, 4QKM


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
influenza M2 monomer	A	27	Influenza A virus (A/udorn/1972(H3N2))	Mutation(s): 2  Membrane Entity: Yes
UniProt
Find proteins for P0DOF5 (Influenza A virus (strain A/Udorn/307/1972 H3N2)) Explore P0DOF5  Go to UniProtKB:  P0DOF5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLB	F [auth A]	(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-QJRAZLAKSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
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: 1.44 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 = 30.09	α = 90
b = 30.09	β = 90
c = 67.39	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-06-06 
• Released Date: 2015-11-11 
Deposition Author(s): Thomaston, J.L., DeGrado, W.F.

Revision History  

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