4R7C

Crystal Structure of CNG mimicking NaK-ETPP mutant cocrystallized with DiMethylammonium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A structural, functional, and computational analysis suggests pore flexibility as the base for the poor selectivity of CNG channels.

Napolitano, L.M.Bisha, I.De March, M.Marchesi, A.Arcangeletti, M.Demitri, N.Mazzolini, M.Rodriguez, A.Magistrato, A.Onesti, S.Laio, A.Torre, V.

(2015) Proc.Natl.Acad.Sci.USA 112: E3619-E3628

  • DOI: 10.1073/pnas.1503334112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cyclic nucleotide-gated (CNG) ion channels, despite a significant homology with the highly selective K(+) channels, do not discriminate among monovalent alkali cations and are permeable also to several organic cations. We combined electrophysiology, ...

    Cyclic nucleotide-gated (CNG) ion channels, despite a significant homology with the highly selective K(+) channels, do not discriminate among monovalent alkali cations and are permeable also to several organic cations. We combined electrophysiology, molecular dynamics (MD) simulations, and X-ray crystallography to demonstrate that the pore of CNG channels is highly flexible. When a CNG mimic is crystallized in the presence of a variety of monovalent cations, including Na(+), Cs(+), and dimethylammonium (DMA(+)), the side chain of Glu66 in the selectivity filter shows multiple conformations and the diameter of the pore changes significantly. MD simulations indicate that Glu66 and the prolines in the outer vestibule undergo large fluctuations, which are modulated by the ionic species and the voltage. This flexibility underlies the coupling between gating and permeation and the poor ionic selectivity of CNG channels.


    Organizational Affiliation

    Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Basovizza, Trieste 34149, Italy;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Potassium channel protein
A, B, C, D
96Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)Mutation(s): 4 
Find proteins for Q81HW2 (Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711))
Go to UniProtKB:  Q81HW2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLY
Query on GLY

Download SDF File 
Download CCD File 
A, B, C, D
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
DMN
Query on DMN

Download SDF File 
Download CCD File 
A, B, C, D
DIMETHYLAMINE
C2 H7 N
ROSDSFDQCJNGOL-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, B, C
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.207 
  • Space Group: P 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 89.891α = 90.00
b = 67.680β = 90.00
c = 67.621γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
Elettradata collection
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-07-22
    Type: Database references
  • Version 1.2: 2018-01-31
    Type: Experimental preparation