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 
  • R-Value Observed: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Structures With Same Primary Citation

  • 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 Na V Ab 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 (Na V Ab/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 Na v Ab/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 Na V Ab/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; wcatt@uw.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ion transport protein
A
244Arcobacter butzleriMutation(s): 0 
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective		Protein: 
Voltage-Gated Sodium Channel (NaV) in closed state (NaVAb/FY)
Find proteins for A8EVM5 (Arcobacter butzleri (strain RM4018))
Go to UniProtKB:  A8EVM5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PX4
Query on PX4
Download CCD File 
A
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C36 H73 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-O		 Ligand Interaction
SO4
Query on SO4
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
NA
Query on NA
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 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 
  • R-Value Observed: 0.230 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.302α = 90
b = 125.302β = 90
c = 192.424γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01 NS15751
Howard Hughes Medical Institute (HHMI)United States--

Revision History 

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-04-19
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.3: 2019-11-20
    Changes: Author supporting evidence