2DWD

crystal structure of KcsA-FAB-TBA complex in Tl+

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.241 

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Literature

Crystallographic Study of the Tetrabutylammonium Block to the KcsA K(+) Channel

Yohannan, S., Hu, Y., Zhou, Y.

(2007) J Mol Biol 366: 806-814

  • DOI: 10.1016/j.jmb.2006.11.081
  • Primary Citation of Related Structures:  
    2DWD, 2DWE, 2HVJ, 2HVK

  • PubMed Abstract: 

    • K(+) channels play essential roles in regulating membrane excitability of many diverse cell types by selectively conducting K(+) ions through their pores. Many diverse molecules can plug the pore and modulate the K(+) current. Quaternary ammonium (QA) ions are a class of pore blockers that have been used for decades by biophysicists to probe the pore, leading to important insights into the structure-function relation of K(+) channels ...

    K(+) channels play essential roles in regulating membrane excitability of many diverse cell types by selectively conducting K(+) ions through their pores. Many diverse molecules can plug the pore and modulate the K(+) current. Quaternary ammonium (QA) ions are a class of pore blockers that have been used for decades by biophysicists to probe the pore, leading to important insights into the structure-function relation of K(+) channels. However, many key aspects of the QA-blocking mechanisms remain unclear to date, and understanding these questions requires high resolution structural information. Here, we address the question of whether intracellular QA blockade causes conformational changes of the K(+) channel selectivity filter. We have solved the structures of the KcsA K(+) channel in complex with tetrabutylammonium (TBA) and tetrabutylantimony (TBSb) under various ionic conditions. Our results demonstrate that binding of TBA or TBSb causes no significant change in the KcsA structure at high concentrations of permeant ions. We did observe the expected conformational change of the filter at low concentration of K(+), but this change appears to be independent of TBA or TBSb blockade.

    Organizational Affiliation: 

    Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ANTIBODY FAB HEAVY CHAINA219Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ANTIBODY FAB LIGHT CHAINB212Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-gated potassium channelC103Streptomyces lividansMutation(s): 1 
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L2C
Query on L2C
Download Ideal Coordinates CCD File 
I [auth C](2S)-3-HYDROXY-2-(NONANOYLOXY)PROPYL LAURATE
C24 H46 O5
MYFVXYUACRBWGD-QFIPXVFZSA-N		 Ligand Interaction
TBA
Query on TBA
Download Ideal Coordinates CCD File 
J [auth C]TETRABUTYLAMMONIUM ION
C16 H36 N
DZLFLBLQUQXARW-UHFFFAOYSA-N		 Ligand Interaction
TL
Query on TL
Download Ideal Coordinates CCD File 
E [auth C],
F [auth C],
G [auth C],
H [auth C]		THALLIUM (I) ION
Tl
ZLUSCZLCHQSJRU-UHFFFAOYSA-N		 Ligand Interaction
F09
Query on F09
Download Ideal Coordinates CCD File 
D [auth A]NONAN-1-OL
C9 H20 O
ZWRUINPWMLAQRD-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.241 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.18α = 90
b = 153.18β = 90
c = 75.483γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2006-08-10 
  • Released Date: 2007-02-20 
    • Deposition Author(s): Yohannan, S., Zhou, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations