4CBC

Open-form NavMS Sodium Channel Pore (with C-terminal Domain) after thallium soak


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.277 

wwPDB Validation 3D Report Full Report


This is version 1.3 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 U S A 111: 8428

  • DOI: 10.1073/pnas.1406855111
  • Primary Citation of Related Structures:  
    4P9O, 4P9P, 4OXS, 4PA6, 4PA7, 4PA9, 4PA3, 4PA4, 4CBC, 4P30

  • 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: 
    • 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.M., 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, School of Biological Sciences, Birkbeck College, University of London, London WC1E 7HX, United Kingdom; dclapham@enders.tch.harvard.edu b.wallace@mail.cryst.bbk.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ION TRANSPORT PROTEINABCD149Magnetococcus marinus MC-1Mutation(s): 0 
Gene Names: Mmc1_0798
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective
Protein: 
Voltage-Gated Sodium Channel (NaV), apo open form
Find proteins for A0L5S6 (Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1))
Explore A0L5S6 
Go to UniProtKB:  A0L5S6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2CV
Query on 2CV

Download CCD File 
A, B, C, D
HEGA-10
C18 H37 N O7
ITEIKACYSCODFV-ATLSCFEFSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.277 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.901α = 90
b = 331.704β = 90
c = 79.933γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2014-06-04
    Changes: Database references
  • Version 1.2: 2014-06-25
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Data collection