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

Experimental Data Snapshot

  • Resolution: 2.66 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.277 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1073/pnas.1406855111
  • Primary Citation of Related Structures:  
    4CBC, 4OXS, 4P2Z, 4P30, 4P9O, 4P9P, 4PA3, 4PA4, 4PA6, 4PA7, 4PA9

  • 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 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
149Magnetococcus marinus MC-1Mutation(s): 0 
Gene Names: Mmc1_0798
Membrane Entity: Yes 
Find proteins for A0L5S6 (Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1))
Explore A0L5S6 
Go to UniProtKB:  A0L5S6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0L5S6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 2CV

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
J [auth B]
K [auth B]
L [auth C]
E [auth A],
F [auth A],
J [auth B],
K [auth B],
L [auth C],
P [auth D]
C18 H37 N O7
Query on NA

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
M [auth C]
N [auth C]
G [auth A],
H [auth A],
I [auth A],
M [auth C],
N [auth C],
O [auth C]
Experimental Data & Validation

Experimental Data

  • 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
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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