5VB8

Crystal structure of the NavAb voltage-gated sodium channel in an open state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of closed and open states of a voltage-gated sodium channel.

Lenaeus, M.J.Gamal El-Din, T.M.Ing, C.Ramanadane, K.Pomes, R.Zheng, N.Catterall, W.A.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: E3051-E3060

  • DOI: 10.1073/pnas.1700761114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial voltage-gated sodium channels (BacNavs) serve as models of their vertebrate counterparts. BacNavs contain conserved voltage-sensing and pore-forming domains, but they are homotetramers of four identical subunits, rather than pseudotetramers ...

    Bacterial voltage-gated sodium channels (BacNavs) serve as models of their vertebrate counterparts. BacNavs contain conserved voltage-sensing and pore-forming domains, but they are homotetramers of four identical subunits, rather than pseudotetramers of four homologous domains. Here, we present structures of two NaVAb mutants that capture tightly closed and open states at a resolution of 2.8-3.2 Å. Introduction of two humanizing mutations in the S6 segment (NaVAb/FY: T206F and V213Y) generates a persistently closed form of the activation gate in which the intracellular ends of the four S6 segments are drawn tightly together to block ion permeation completely. This construct also revealed the complete structure of the four-helix bundle that forms the C-terminal domain. In contrast, truncation of the C-terminal 40 residues in NavAb/1-226 captures the activation gate in an open conformation, revealing the open state of a BacNav with intact voltage sensors. Comparing these structures illustrates the full range of motion of the activation gate, from closed with its orifice fully occluded to open with an orifice of ∼10 Å. Molecular dynamics and free-energy simulations confirm designation of NaVAb/1-226 as an open state that allows permeation of hydrated Na+, and these results also support a hydrophobic gating mechanism for control of ion permeation. These two structures allow completion of a closed-open-inactivated conformational cycle in a single voltage-gated sodium channel and give insight into the structural basis for state-dependent binding of sodium channel-blocking drugs.


    Organizational Affiliation

    Department of Pharmacology, University of Washington, Seattle, WA 98195.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ion transport protein
A
244Arcobacter butzleri (strain RM4018)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), I217C mutant
Find proteins for A8EVM5 (Arcobacter butzleri (strain RM4018))
Go to UniProtKB:  A8EVM5
Small Molecules
Ligands 3 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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PX4
Query on PX4

Download SDF File 
Download CCD File 
A
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C36 H73 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.228 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 125.302α = 90.00
b = 125.302β = 90.00
c = 192.424γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and StrokeUnited StatesR01 NS15751
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-04-19
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence