5XSY

Structure of the Nav1.4-beta1 complex from electric eel


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the Nav1.4-beta 1 Complex from Electric Eel.

Yan, Z.Zhou, Q.Wang, L.Wu, J.Zhao, Y.Huang, G.Peng, W.Shen, H.Lei, J.Yan, N.

(2017) Cell 170: 470-482.e11

  • DOI: 10.1016/j.cell.2017.06.039

  • PubMed Abstract: 
  • Voltage-gated sodium (Na <sub>v </sub>) channels initiate and propagate action potentials. Here, we present the cryo-EM structure of EeNa <sub>v </sub>1.4, the Na <sub>v </sub> channel from electric eel, in complex with the β1 subunit at 4.0 Å resolu ...

    Voltage-gated sodium (Na v ) channels initiate and propagate action potentials. Here, we present the cryo-EM structure of EeNa v 1.4, the Na v channel from electric eel, in complex with the β1 subunit at 4.0 Å resolution. The immunoglobulin domain of β1 docks onto the extracellular L5 I and L6 IV loops of EeNa v 1.4 via extensive polar interactions, and the single transmembrane helix interacts with the third voltage-sensing domain (VSD III ). The VSDs exhibit "up" conformations, while the intracellular gate of the pore domain is kept open by a digitonin-like molecule. Structural comparison with closed Na v PaS shows that the outward transfer of gating charges is coupled to the iris-like pore domain dilation through intricate force transmissions involving multiple channel segments. The IFM fast inactivation motif on the III-IV linker is plugged into the corner enclosed by the outer S4-S5 and inner S6 segments in repeats III and IV, suggesting a potential allosteric blocking mechanism for fast inactivation.


    Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.,State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China; Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China. Electronic address: nyan@tsinghua.edu.cn.,Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China; Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, China.,State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China; Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sodium channel protein
A
1820Electrophorus electricusMutation(s): 0 
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective
Protein: 
NaV1.4-β1 complex
Find proteins for P02719 (Electrophorus electricus)
Go to UniProtKB:  P02719
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Voltage-gated sodium channel beta subunit 1
B
209Electrophorus electricusMutation(s): 0 
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective
Protein: 
NaV1.4-β1 complex
Find proteins for A0A1L3MZ94 (Electrophorus electricus)
Go to UniProtKB:  A0A1L3MZ94
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology of ChinaChina2015CB910101, 2016YFA0500402, 2014ZX09507003-006
National Natural Science Foundation of ChinaChinaprojects 31621092, 31630017, 31611130036

Revision History 

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Data collection, Other, Refinement description