4PA6

Structure of NavMS pore and C-terminal domain crystallised in the presence of channel blocking compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.36 Å
  • R-Value Free: 0.342 
  • R-Value Work: 0.302 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Prokaryotic NavMs channel as a structural and functional model for eukaryotic sodium channel antagonism.

Bagneris, C.DeCaen, P.G.Naylor, C.E.Pryde, D.C.Nobeli, I.Clapham, D.E.Wallace, B.A.

(2014) Proc.Natl.Acad.Sci.USA 111: 8428-8433

  • DOI: 10.1073/pnas.1406855111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Voltage-gated sodium channels are important targets for the development of pharmaceutical drugs, because mutations in different human sodium channel isoforms have causal relationships with a range of neurological and cardiovascular diseases. In this ...

    Voltage-gated sodium channels are important targets for the development of pharmaceutical drugs, because mutations in different human sodium channel isoforms have causal relationships with a range of neurological and cardiovascular diseases. In this study, functional electrophysiological studies show that the prokaryotic sodium channel from Magnetococcus marinus (NavMs) binds and is inhibited by eukaryotic sodium channel blockers in a manner similar to the human Nav1.1 channel, despite millions of years of divergent evolution between the two types of channels. Crystal complexes of the NavMs pore with several brominated blocker compounds depict a common antagonist binding site in the cavity, adjacent to lipid-facing fenestrations proposed to be the portals for drug entry. In silico docking studies indicate the full extent of the blocker binding site, and electrophysiology studies of NavMs channels with mutations at adjacent residues validate the location. These results suggest that the NavMs channel can be a valuable tool for screening and rational design of human drugs.


    Related Citations: 
    • 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
    • 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


    Organizational Affiliation

    Institute of Structural and Molecular Biology, School of Biological Sciences, Birkbeck College, University of London, London WC1E 7HX, United Kingdom;




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 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective
Protein: 
Voltage-Gated Sodium Channel (NaV)
Find proteins for A0L5S6 (Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1))
Go to UniProtKB:  A0L5S6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
12P
Query on 12P

Download SDF File 
Download CCD File 
A
DODECAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C24 H50 O13
WRZXKWFJEFFURH-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: 3.36 Å
  • R-Value Free: 0.342 
  • R-Value Work: 0.302 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 79.934α = 90.00
b = 324.571β = 90.00
c = 79.766γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement

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: 2014-06-04
    Type: Initial release
  • Version 1.1: 2014-08-06
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy