5BZB

NavMs voltage-gated sodium channel pore and C-terminal domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.15252/embj.201593285
  • Primary Citation of Related Structures:  
    4X88, 4X89, 4X8A, 5BZB

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ion transport protein
A, B, C, D
149Magnetococcus marinus MC-1Mutation(s): 0 
Gene Names: Mmc1_0798
Membrane Entity: Yes 
UniProt
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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
12P
Query on 12P

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
L [auth C]
DODECAETHYLENE GLYCOL
C24 H50 O13
WRZXKWFJEFFURH-UHFFFAOYSA-N
2CV
Query on 2CV

Download Ideal Coordinates CCD File 
I [auth B],
J [auth B],
O [auth D],
P [auth D]
HEGA-10
C18 H37 N O7
ITEIKACYSCODFV-ATLSCFEFSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
M [auth C]
N [auth C]
F [auth A],
G [auth A],
H [auth A],
M [auth C],
N [auth C],
Q [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.34α = 90
b = 332.763β = 90
c = 80.38γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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  (Full details and data files)

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-04-27
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Author supporting evidence
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description