3IGA

Potassium Channel KcsA-Fab complex in Li+ and K+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Mechanism of potassium-channel selectivity revealed by Na(+) and Li(+) binding sites within the KcsA pore.

Thompson, A.N.Kim, I.Panosian, T.D.Iverson, T.M.Allen, T.W.Nimigean, C.M.

(2009) Nat.Struct.Mol.Biol. 16: 1317-1324

  • DOI: 10.1038/nsmb.1703
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Potassium channels allow K(+) ions to diffuse through their pores while preventing smaller Na(+) ions from permeating. Discrimination between these similar, abundant ions enables these proteins to control electrical and chemical activity in all organ ...

    Potassium channels allow K(+) ions to diffuse through their pores while preventing smaller Na(+) ions from permeating. Discrimination between these similar, abundant ions enables these proteins to control electrical and chemical activity in all organisms. Selection occurs at the narrow selectivity filter containing structurally identified K(+) binding sites. Selectivity is thought to arise because smaller ions such as Na(+) do not bind to these K(+) sites in a thermodynamically favorable way. Using the model K(+) channel KcsA, we examined how intracellular Na(+) and Li(+) interact with the pore and the permeant ions using electrophysiology, molecular dynamics simulations and X-ray crystallography. Our results suggest that these small cations have a separate binding site within the K(+) selectivity filter. We propose that selective permeation from the intracellular side primarily results from a large energy barrier blocking filter entry for Na(+) and Li(+) in the presence of K(+), not from a difference of binding affinity between ions.


    Organizational Affiliation

    Department of Anesthesiology, Weill Cornell Medical College, New York, New York, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antibody Fab 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 Fab 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
124Streptomyces lividansMutation(s): 2 
Gene Names: kcsA (skc1)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective
Protein: 
KcsA Potassium channel, H+ gated
Find proteins for P0A334 (Streptomyces lividans)
Go to UniProtKB:  P0A334
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGA
Query on DGA

Download SDF File 
Download CCD File 
C
DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
C
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.242 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 155.799α = 90.00
b = 155.799β = 90.00
c = 75.775γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-09-25
    Type: Derived calculations
  • Version 1.3: 2018-01-24
    Type: Advisory, Structure summary