2JK5

Potassium Channel KcsA in complex with Tetrabutylammonium in high K

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

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Literature

Structures of Kcsa in Complex with Symmetrical Quaternary Ammonium Compounds Reveal a Hydrophobic Binding Site.

Lenaeus, M.J., Burdette, D., Wagner, T., Focia, P.J., Gross, A.

(2014) Biochemistry 53: 5365

  • DOI: 10.1021/bi500525s
  • Primary Citation of Related Structures:  
    2JK5, 2W0F, 4UUJ

  • PubMed Abstract: 

    • Potassium channels allow for the passive movement of potassium ions across the cell membrane and are instrumental in controlling the membrane potential in all cell types. Quaternary ammonium (QA) compounds block potassium channels and have long been used to study the functional and structural properties of these channels ...

    Potassium channels allow for the passive movement of potassium ions across the cell membrane and are instrumental in controlling the membrane potential in all cell types. Quaternary ammonium (QA) compounds block potassium channels and have long been used to study the functional and structural properties of these channels. Here we describe the interaction between three symmetrical hydrophobic QAs and the prokaryotic potassium channel KcsA. The structures demonstrate the presence of a hydrophobic pocket between the inner helices of KcsA and provide insight into the binding site and blocking mechanism of hydrophobic QAs. The structures also reveal a structurally hidden pathway between the central cavity and the outside membrane environment reminiscent of the lateral fenestration observed in sodium channels that can be accessed through small conformational changes in the pore wall. We propose that the hydrophobic binding pocket stabilizes the alkyl chains of long-chain QA molecules and may play a key role in hydrophobic drug binding in general.

    Organizational Affiliation: 

    Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Medical School , 303 East Chicago Avenue, Chicago, Illinois 60611, United States.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ANTIBODY FAB FRAGMENT LIGHT CHAINA219Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ANTIBODY FAB FRAGMENT HEAVY CHAINB212Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
VOLTAGE-GATED POTASSIUM CHANNELC124Streptomyces lividansMutation(s): 0 
Gene Names: kcsA, skc1
Membrane Entity: Yes 
UniProt
Find proteins for P0A334 (Streptomyces lividans)
Explore P0A334 
Go to UniProtKB:  P0A334
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A334
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L2C
Query on L2C
Download Ideal Coordinates CCD File 
L [auth C](2S)-3-HYDROXY-2-(NONANOYLOXY)PROPYL LAURATE
C24 H46 O5
MYFVXYUACRBWGD-QFIPXVFZSA-N		 Ligand Interaction
TBA
Query on TBA
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M [auth C]TETRABUTYLAMMONIUM ION
C16 H36 N
DZLFLBLQUQXARW-UHFFFAOYSA-N		 Ligand Interaction
F09
Query on F09
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K [auth C]NONAN-1-OL
C9 H20 O
ZWRUINPWMLAQRD-UHFFFAOYSA-N		 Ligand Interaction
HP6
Query on HP6
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N [auth C]HEPTANE
C7 H16
IMNFDUFMRHMDMM-UHFFFAOYSA-N		 Ligand Interaction
CO
Query on CO
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D [auth C]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N		 Ligand Interaction
K
Query on K
Download Ideal Coordinates CCD File 
E [auth C],
F [auth C],
G [auth C],
H [auth C],
I [auth C],
E [auth C],
F [auth C],
G [auth C],
H [auth C],
I [auth C],
J [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.145α = 90
b = 156.145β = 90
c = 76.326γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2014-08-27
    Changes: Database references, Derived calculations, Other, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2014-09-03
    Changes: Database references