2DWE | pdb_00002dwe

Crystal structure of KcsA-FAB-TBA complex in Rb+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.266 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.245 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

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

Yohannan, S.Hu, Y.Zhou, Y.

(2007) J Mol Biology 366: 806-814

  • DOI: https://doi.org/10.1016/j.jmb.2006.11.081
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 58.88 kDa 
  • Atom Count: 4,223 
  • Modeled Residue Count: 534 
  • Deposited Residue Count: 534 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ANTIBODY FAB HEAVY CHAIN219Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ANTIBODY FAB LIGHT CHAIN212Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Voltage-gated potassium channel103Streptomyces lividansMutation(s): 1 
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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L2C

Query on L2C



Download:Ideal Coordinates CCD File
G [auth C](2S)-3-HYDROXY-2-(NONANOYLOXY)PROPYL LAURATE
C24 H46 O5
MYFVXYUACRBWGD-QFIPXVFZSA-N
TBA

Query on TBA



Download:Ideal Coordinates CCD File
I [auth C]TETRABUTYLAMMONIUM ION
C16 H36 N
DZLFLBLQUQXARW-UHFFFAOYSA-N
F09

Query on F09



Download:Ideal Coordinates CCD File
H [auth C]NONAN-1-OL
C9 H20 O
ZWRUINPWMLAQRD-UHFFFAOYSA-N
RB

Query on RB



Download:Ideal Coordinates CCD File
D [auth C],
E [auth C],
F [auth C]
RUBIDIUM ION
Rb
NCCSSGKUIKYAJD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.266 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.245 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.56α = 90
b = 154.56β = 90
c = 75.813γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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
  • Version 1.4: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-11-20
    Changes: Structure summary