3IFX

Crystal structure of the Spin-labeled KcsA mutant V48R1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.56 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.273 

    wwPDB Validation 3D Report Full Report


    This is version 1.2 of the entry. See complete history


    Literature

    Electron Spin-Echo Envelope Modulation (ESEEM) Reveals Water and Phosphate Interactions with the KcsA Potassium Channel

    Cieslak, J.A.Focia, P.J.Gross, A.

    (2010) Biochemistry 49: 1486-1494

    • DOI: 10.1021/bi9016523
    • Primary Citation of Related Structures:  
      3IFX

    • PubMed Abstract: 
    • Electron spin-echo envelope modulation (ESEEM) spectroscopy is a well-established technique for the study of naturally occurring paramagnetic metal centers. The technique has been used to study copper complexes, hemes, enzyme mechanisms, micellar wat ...

      Electron spin-echo envelope modulation (ESEEM) spectroscopy is a well-established technique for the study of naturally occurring paramagnetic metal centers. The technique has been used to study copper complexes, hemes, enzyme mechanisms, micellar water content, and water permeation profiles in membranes, among other applications. In the present study, we combine ESEEM spectroscopy with site-directed spin labeling (SDSL) and X-ray crystallography in order to evaluate the technique's potential as a structural tool to describe the native environment of membrane proteins. Using the KcsA potassium channel as a model system, we demonstrate that deuterium ESEEM can detect water permeation along the lipid-exposed surface of the KcsA outer helix. We further demonstrate that (31)P ESEEM is able to identify channel residues that interact with the phosphate headgroup of the lipid bilayer. In combination with X-ray crystallography, the (31)P data may be used to define the phosphate interaction surface of the protein. The results presented here establish ESEEM as a highly informative technique for SDSL studies of membrane proteins.


      Organizational Affiliation

      Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, 303 East Chicago Avenue, Chicago, Illinois 60611, USA.



    Macromolecules
    Find similar proteins by:  (by identity cutoff)  |  Structure
    Entity ID: 1
    MoleculeChainsSequence LengthOrganismDetailsImage
    Voltage-gated potassium channelA, B, C, D129Streptomyces lividansMutation(s): 1 
    Gene Names: kcsAskc1
    Find proteins for P0A334 (Streptomyces lividans)
    Explore P0A334 
    Go to UniProtKB:  P0A334
    Protein Feature View
     ( Mouse scroll to zoom / Hold left click to move )
    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MTN
    Query on MTN

    Download CCD File 
    A, B, C, D
    S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate
    C10 H18 N O3 S2
    MXZPGYFBZHBAQM-UHFFFAOYSA-N
     Ligand Interaction
    TBA
    Query on TBA

    Download CCD File 
    B
    TETRABUTYLAMMONIUM ION
    C16 H36 N
    DZLFLBLQUQXARW-UHFFFAOYSA-N
     Ligand Interaction
    K
    Query on K

    Download CCD File 
    A, B
    POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.56 Å
    • R-Value Free: 0.302 
    • R-Value Work: 0.271 
    • R-Value Observed: 0.273 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 130.97α = 90
    b = 76.63β = 125.83
    c = 112.97γ = 90
    Software Package:
    Software NamePurpose
    MOSFLMdata reduction
    PHASERphasing
    REFMACrefinement
    SCALAdata scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2010-02-09
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance
    • Version 1.2: 2011-07-27
      Changes: Advisory, Non-polymer description, Refinement description