3ZJZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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

  • DOI: 10.1038/ncomms3465
  • Also Cited By: 5HVX, 5HVD, 5BZB, 4X8A, 4X89, 4X88, 4PA9, 4PA7, 4PA6, 4PA4, 4PA3, 4P9P, 4P9O, 4P30, 4P2Z, 4OXS, 4CBC

  • PubMed Abstract: 
  • Voltage-gated sodium channels have essential roles in electrical signalling. Prokaryotic sodium channels are tetramers consisting of transmembrane (TM) voltage-sensing and pore domains, and a cytoplasmic carboxy-terminal domain. Previous crystal stru ...

    Voltage-gated sodium channels have essential roles in electrical signalling. Prokaryotic sodium channels are tetramers consisting of transmembrane (TM) voltage-sensing and pore domains, and a cytoplasmic carboxy-terminal domain. Previous crystal structures of bacterial sodium channels revealed the nature of their TM domains but not their C-terminal domains (CTDs). Here, using electron paramagnetic resonance (EPR) spectroscopy combined with molecular dynamics, we show that the CTD of the NavMs channel from Magnetococcus marinus includes a flexible region linking the TM domains to a four-helix coiled-coil bundle. A 2.9 Å resolution crystal structure of the NavMs pore indicates the position of the CTD, which is consistent with the EPR-derived structure. Functional analyses demonstrate that the coiled-coil domain couples inactivation with channel opening, and is enabled by negatively charged residues in the linker region. A mechanism for gating is proposed based on the structure, whereby splaying of the bottom of the pore is possible without requiring unravelling of the coiled-coil.


    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


    Organizational Affiliation

    1] School of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK [2].




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, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
12P
Query on 12P

Download SDF File 
Download CCD File 
A, B, C
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: 2.92 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.257 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 80.150α = 90.00
b = 334.380β = 90.00
c = 80.210γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-02
    Type: Initial release