3E86

High resolution Crystal Structure of the open NaK channel pore

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

High-resolution structure of the open NaK channel

Alam, A., Jiang, Y.

(2009) Nat Struct Mol Biol 16: 30-34

  • DOI: 10.1038/nsmb.1531
  • Primary Citation of Related Structures:  
    3E86

  • PubMed Abstract: 

    • We report the crystal structure of the nonselective cation channel NaK from Bacillus cereus at a resolution of 1.6 A. The structure reveals the intracellular gate in an open state, as opposed to the closed form reported previously, making NaK the onl ...

    We report the crystal structure of the nonselective cation channel NaK from Bacillus cereus at a resolution of 1.6 A. The structure reveals the intracellular gate in an open state, as opposed to the closed form reported previously, making NaK the only channel for which the three-dimensional structures of both conformations are known. Channel opening follows a conserved mechanism of inner helix bending using a flexible glycine residue, the gating hinge, seen in MthK and most other tetrameric cation channels. Additionally, distinct inter and intrasubunit rearrangements involved in channel gating are seen and characterized for the first time along with inner helix twisting motions. Furthermore, we identify a residue deeper within the cavity of the channel pore, Phe92, which is likely to form a constriction point within the open pore, restricting ion flux through the channel. Mutating this residue to alanine causes a subsequent increase in ion-conduction rates as measured by (86)Rb flux assays. The structures of both the open and closed conformations of the NaK channel correlate well with those of equivalent K(+) channel conformations, namely MthK and KcsA, respectively.

    Organizational Affiliation: 

    Department of Physiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9040, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Potassium channel proteinA, B96Bacillus cereusMutation(s): 0 
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective		Protein: 
NaK channel in open state (NΔ19 mutant)
Find proteins for Q81HW2 (Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711))
Explore Q81HW2 
Go to UniProtKB:  Q81HW2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.212 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.03α = 90
b = 68.03β = 90
c = 89.264γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2008-08-19 
  • Released Date: 2008-12-23 
    • Deposition Author(s): Jiang, Y., Alam, A.

Revision History 

  • Version 1.0: 2008-12-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-11-16
    Changes: Atomic model
  • Version 1.3: 2017-10-25
    Changes: Refinement description