4LTQ

Bacterial sodium channel in low calcium, P42 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.50 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.268 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a prokaryotic sodium channel pore reveals essential gating elements and an outer ion binding site common to eukaryotic channels.

Shaya, D.Findeisen, F.Abderemane-Ali, F.Arrigoni, C.Wong, S.Nurva, S.R.Loussouarn, G.Minor, D.L.

(2014) J Mol Biol 426: 467-483

  • DOI: 10.1016/j.jmb.2013.10.010
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Voltage-gated sodium channels (NaVs) are central elements of cellular excitation. Notwithstanding advances from recent bacterial NaV (BacNaV) structures, key questions about gating and ion selectivity remain. Here, we present a closed conformation of ...

    Voltage-gated sodium channels (NaVs) are central elements of cellular excitation. Notwithstanding advances from recent bacterial NaV (BacNaV) structures, key questions about gating and ion selectivity remain. Here, we present a closed conformation of NaVAe1p, a pore-only BacNaV derived from NaVAe1, a BacNaV from the arsenite oxidizer Alkalilimnicola ehrlichei found in Mono Lake, California, that provides insight into both fundamental properties. The structure reveals a pore domain in which the pore-lining S6 helix connects to a helical cytoplasmic tail. Electrophysiological studies of full-length BacNaVs show that two elements defined by the NaVAe1p structure, an S6 activation gate position and the cytoplasmic tail "neck", are central to BacNaV gating. The structure also reveals the selectivity filter ion entry site, termed the "outer ion" site. Comparison with mammalian voltage-gated calcium channel (CaV) selectivity filters, together with functional studies, shows that this site forms a previously unknown determinant of CaV high-affinity calcium binding. Our findings underscore commonalities between BacNaVs and eukaryotic voltage-gated channels and provide a framework for understanding gating and ion permeation in this superfamily.


    Organizational Affiliation

    Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001, USA; Departments of Biochemistry and Biophysics and Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158-9001, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158-9001, USA; Physical Biosciences Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: daniel.minor@ucsf.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ion transport protein
A, B, C, D, H, I, J, K
152Alkalilimnicola ehrlichiiMutation(s): 0 
Gene Names: Mlg_0322
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective
Protein: 
NaVAe1p pore-only volt-gated sodium channel (crystal I; I222 space group; high Ca2+)
Find proteins for Q0ABW0 (Alkalilimnicola ehrlichii (strain ATCC BAA-1101 / DSM 17681 / MLHE-1))
Go to UniProtKB:  Q0ABW0
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.50 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.268 
  • Space Group: P 42
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.136α = 90
b = 181.136β = 90
c = 94.021γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2013-11-06
    Changes: Database references
  • Version 1.2: 2014-01-22
    Changes: Database references