6W0G

Closed-gate KcsA soaked in 1mM KCl/5mM BaCl2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

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Literature

Open and Closed Structures of a Barium-Blocked Potassium Channel.

Rohaim, A.Gong, L.Li, J.Rui, H.Blachowicz, L.Roux, B.

(2020) J Mol Biol 432: 4783-4798

  • DOI: https://doi.org/10.1016/j.jmb.2020.06.012
  • Primary Citation of Related Structures:  
    6W0A, 6W0B, 6W0C, 6W0D, 6W0E, 6W0F, 6W0G, 6W0H, 6W0I, 6W0J

  • PubMed Abstract: 

    Barium (Ba 2+ ) is a classic permeant blocker of potassium (K + ) channels. The "external lock-in effect" in barium block experiments, whereby the binding of external K + impedes the forward translocation of the blocker, provides a powerful avenue to investigate the selectivity of the binding sites along the pore of potassium channels. Barium block experiments show that the external lock-in site is highly selective for K + over Na + . Wild-type KcsA was crystallized in low K + conditions, and the crystals were soaked in solutions containing various concentrations of barium. Structural analysis reveals open and closed gate conformations of the KcsA channel. Anomalous diffraction experiments show that Ba 2+ primarily binds to the innermost site S4 of the selectivity filter of the open-gate conformation and also the site S2, but no binding is detected with the closed-gate conformation. Alchemical free-energy perturbation calculations indicate that the presence of a Ba 2+ ion in the selectivity filter boosts the specificity of K + binding relative to Na + in the external sites S0-S2.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Chicago, Gordon Center for Integrative Science, 929 E 57th St, Chicago, IL 60637, USA; Department of Biophysics, Faculty of Science, Cairo University, Giza 12613, Egypt.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab Heavy Chain219Rattus norvegicusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab Light Chain212Rattus norvegicusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
pH-gated potassium channel KcsA103Streptomyces lividansMutation(s): 1 
Gene Names: kcsAskc1
Membrane Entity: Yes 
UniProt
Find proteins for P0A334 (Streptomyces lividans)
Explore P0A334 
Go to UniProtKB:  P0A334
Entity Groups  
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UniProt GroupP0A334
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K (Subject of Investigation/LOI)
Query on K

Download Ideal Coordinates CCD File 
D [auth C]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.138α = 90
b = 155.138β = 90
c = 75.38γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Database references
  • Version 1.2: 2020-08-19
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description