2HJF

Potassium channel kcsa-fab complex with tetrabutylammonium (TBA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism of Intracellular Block of the KcsA K(+) Channel by Tetrabutylammonium: Insights from X-ray Crystallography, Electrophysiology and Replica-exchange Molecular Dynamics Simulations.

Faraldo-Gomez, J.D.Kutluay, E.Jogini, V.Zhao, Y.Heginbotham, L.Roux, B.

(2007) J.Mol.Biol. 365: 649-662

  • DOI: 10.1016/j.jmb.2006.09.069

  • PubMed Abstract: 
  • The mechanism of intracellular blockade of the KcsA potassium channel by tetrabutylammonium (TBA) is investigated through functional, structural and computational studies. Using planar-membrane electrophysiological recordings, we characterize the bin ...

    The mechanism of intracellular blockade of the KcsA potassium channel by tetrabutylammonium (TBA) is investigated through functional, structural and computational studies. Using planar-membrane electrophysiological recordings, we characterize the binding kinetics as well as the dependence on the transmembrane voltage and the concentration of the blocker. It is found that the apparent affinity of the complex is significantly greater than that of any of the eukaryotic K(+) channels studied previously, and that the off-rate increases with the applied transmembrane voltage. In addition, we report a crystal structure of the KcsA-TBA complex at 2.9 A resolution, with TBA bound inside the large hydrophobic cavity located at the center of the channel, consistent with the results of previous functional and structural studies. Of particular interest is the observation that the presence of TBA has a negligible effect on the channel structure and on the position of the potassium ions occupying the selectivity filter. Inspection of the electron density corresponding to TBA suggests that the ligand may adopt more than one conformation in the complex, though the moderate resolution of the data precludes a definitive interpretation on the basis of the crystallographic refinement methods alone. To provide a rationale for these observations, we carry out an extensive conformational sampling of an atomic model of TBA bound in the central cavity of KcsA, using the Hamiltonian replica-exchange molecular dynamics simulation method. Comparison of the simulated and experimental density maps indicates that the latter does reflect at least two distinct binding orientations of TBA. The simulations show also that the relative population of these binding modes is dependent on the ion configuration occupying the selectivity filter, thus providing a clue to the nature of the voltage-dependence of the binding kinetics.


    Organizational Affiliation

    Institute for Molecular Pediatric Sciences and Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Sciences, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antibody fragment Heavy chain
A
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antibody fragment Light chain
B
212N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Voltage-gated potassium channel
C
103Streptomyces lividansMutation(s): 1 
Gene Names: kcsA (skc1)
Find proteins for P0A334 (Streptomyces lividans)
Go to UniProtKB:  P0A334
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
TBA
Query on TBA

Download SDF File 
Download CCD File 
C
TETRABUTYLAMMONIUM ION
C16 H36 N
DZLFLBLQUQXARW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.225 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 156.200α = 90.00
b = 156.200β = 90.00
c = 76.316γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data scaling
CNSphasing
HKL-2000data reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance