5HVD

Full length Open-form Sodium Channel NavMs I218C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The complete structure of an activated open sodium channel.

Sula, A.Booker, J.Ng, L.C.Naylor, C.E.DeCaen, P.G.Wallace, B.A.

(2017) Nat Commun 8: 14205-14205

  • DOI: 10.1038/ncomms14205
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Voltage-gated sodium channels (Navs) play essential roles in excitable tissues, with their activation and opening resulting in the initial phase of the action potential. The cycling of Navs through open, closed and inactivated states, and their close ...

    Voltage-gated sodium channels (Navs) play essential roles in excitable tissues, with their activation and opening resulting in the initial phase of the action potential. The cycling of Navs through open, closed and inactivated states, and their closely choreographed relationships with the activities of other ion channels lead to exquisite control of intracellular ion concentrations in both prokaryotes and eukaryotes. Here we present the 2.45 Å resolution crystal structure of the complete NavMs prokaryotic sodium channel in a fully open conformation. A canonical activated conformation of the voltage sensor S4 helix, an open selectivity filter leading to an open activation gate at the intracellular membrane surface and the intracellular C-terminal domain are visible in the structure. It includes a heretofore unseen interaction motif between W77 of S3, the S4-S5 interdomain linker, and the C-terminus, which is associated with regulation of opening and closing of the intracellular gate.


    Related Citations: 
    • Role of the C-terminal domain in the structure and function of tetrameric sodium channels.
      Bagneris, C.
      (2013) Nat Commun 4: 2465


    Organizational Affiliation

    Department of Pharmacology, Feinberg School of Medicine, Northwestern University, 320 E Superior, Chicago, Illinois 60611, USA.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ion transport protein
A
277Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1)Mutation(s): 1 
Find proteins for A0L5S6 (Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1))
Go to UniProtKB:  A0L5S6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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

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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
HEGA-10
C18 H37 N O7
ITEIKACYSCODFV-ATLSCFEFSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.193 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 109.580α = 90.00
b = 109.580β = 90.00
c = 209.710γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
BUSTERrefinement
XDSdata scaling

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/L02625/21
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/L006790

Revision History 

  • Version 1.0: 2017-03-01
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Author supporting evidence, Data collection