4LTP

Bacterial sodium channel in high calcium, I222 space group, crystal 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.225 

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
  • Primary Citation of Related Structures:  4LTO, 4LTQ, 4LTR

  • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ion transport protein
A, B, C, D
152Alkalilimnicola ehrlichii (strain ATCC BAA-1101 / DSM 17681 / MLHE-1)N/A
Membrane protein
mpstruct
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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.225 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 147.265α = 90.00
b = 161.499β = 90.00
c = 161.690γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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