4X89

NavMs voltage-gated sodium channal pore and C-terminal domain soaked with Silver nitrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Molecular basis of ion permeability in a voltage-gated sodium channel.

Naylor, C.E.Bagneris, C.DeCaen, P.G.Sula, A.Scaglione, A.Clapham, D.E.Wallace, B.A.

(2016) Embo J. 35: 820-830

  • DOI: 10.15252/embj.201593285
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Voltage-gated sodium channels are essential for electrical signalling across cell membranes. They exhibit strong selectivities for sodium ions over other cations, enabling the finely tuned cascade of events associated with action potentials. This pap ...

    Voltage-gated sodium channels are essential for electrical signalling across cell membranes. They exhibit strong selectivities for sodium ions over other cations, enabling the finely tuned cascade of events associated with action potentials. This paper describes the ion permeability characteristics and the crystal structure of a prokaryotic sodium channel, showing for the first time the detailed locations of sodium ions in the selectivity filter of a sodium channel. Electrostatic calculations based on the structure are consistent with the relative cation permeability ratios (Na(+) ≈ Li(+) ≫ K(+), Ca(2+), Mg(2+)) measured for these channels. In an E178D selectivity filter mutant constructed to have altered ion selectivities, the sodium ion binding site nearest the extracellular side is missing. Unlike potassium ions in potassium channels, the sodium ions in these channels appear to be hydrated and are associated with side chains of the selectivity filter residues, rather than polypeptide backbones.


    Related Citations: 
    • Role of the C-terminal domain in the structure and function of tetrameric sodium channels.
      Bagneris, C.,Decaen, P.G.,Hall, B.A.,Naylor, C.E.,Clapham, D.E.,Kay, C.W.,Wallace, B.A.
      (2013) Nat Commun 4: 2465
    • Structure of a bacterial voltage-gated sodium channel pore reveals mechanisms of opening and closing.
      McCusker, E.C.,Bagneris, C.,Naylor, C.E.,Cole, A.R.,D'Avanzo, N.,Nichols, C.G.,Wallace, B.A.
      (2012) Nat Commun 3: 1102


    Organizational Affiliation

    Institute of Structural and Molecular Biology, Birkbeck College University of London, London, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ion transport protein
A, B, C, D
149Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1)Mutation(s): 0 
Find proteins for A0L5S6 (Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1))
Go to UniProtKB:  A0L5S6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
AG
Query on AG

Download SDF File 
Download CCD File 
C
SILVER ION
Ag
FOIXSVOLVBLSDH-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

Download SDF File 
Download CCD File 
A, B, C, D
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
2CV
Query on 2CV

Download SDF File 
Download CCD File 
A, B, C, D
HEGA-10
C18 H37 N O7
ITEIKACYSCODFV-ATLSCFEFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.228 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 80.000α = 90.00
b = 329.240β = 90.00
c = 80.020γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
BUSTERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/H01070X
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J020702

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-06-22
    Type: Database references
  • Version 2.0: 2017-08-30
    Type: Advisory, Atomic model, Author supporting evidence, Derived calculations