5WKV

Structure of an acid sensing ion channel in a resting state with calcium

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Gallus gallus
  • Expression System: Homo sapiens

  • Deposited: 2017-07-25 Released: 2018-03-14 
  • Deposition Author(s): Yoder, N., Gouaux, E.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease; National Institutes of Health/National Institute of Neurological Disorders and Stroke 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.287 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Gating mechanisms of acid-sensing ion channels.

Yoder, N.Yoshioka, C.Gouaux, E.

(2018) Nature 555: 397-401

  • DOI: 10.1038/nature25782
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Acid-sensing ion channels (ASICs) are trimeric, proton-gated and sodium-selective members of the epithelial sodium channel/degenerin (ENaC/DEG) superfamily of ion channels and are expressed throughout vertebrate central and peripheral nervous systems ...

    Acid-sensing ion channels (ASICs) are trimeric, proton-gated and sodium-selective members of the epithelial sodium channel/degenerin (ENaC/DEG) superfamily of ion channels and are expressed throughout vertebrate central and peripheral nervous systems. Gating of ASICs occurs on a millisecond time scale and the mechanism involves three conformational states: high pH resting, low pH open and low pH desensitized. Existing X-ray structures of ASIC1a describe the conformations of the open and desensitized states, but the structure of the high pH resting state and detailed mechanisms of the activation and desensitization of the channel have remained elusive. Here we present structures of the high pH resting state of homotrimeric chicken (Gallus gallus) ASIC1a, determined by X-ray crystallography and single particle cryo-electron microscopy, and present a comprehensive molecular mechanism for proton-dependent gating in ASICs. In the resting state, the position of the thumb domain is further from the three-fold molecular axis, thereby expanding the 'acidic pocket' in comparison to the open and desensitized states. Activation therefore involves 'closure' of the thumb into the acidic pocket, expansion of the lower palm domain and an iris-like opening of the channel gate. Furthermore, we demonstrate how the β11-β12 linkers that demarcate the upper and lower palm domains serve as a molecular 'clutch', and undergo a simple rearrangement to permit rapid desensitization.


    Organizational Affiliation

    Vollum Institute, Oregon Health and Science University, Portland, Oregon 97239, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acid-sensing ion channel 1
A, C, B
439Gallus gallusMutation(s): 0 
Gene Names: ASIC1 (ACCN2)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
ASIC1 Acid-Sensing Ion Channel (ΔASIC1; N- and C-term deletions)
Find proteins for Q1XA76 (Gallus gallus)
Go to Gene View: ASIC1
Go to UniProtKB:  Q1XA76
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.287 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 109.180α = 90.00
b = 133.700β = 90.00
c = 157.650γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-07-25 
  • Released Date: 2018-03-14 
  • Deposition Author(s): Yoder, N., Gouaux, E.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited States5T32DK007680
National Institutes of Health/National Institute of Neurological Disorders and StrokeUnited States5F31NS096782
National Institutes of Health/National Institute of Neurological Disorders and StrokeUnited States5R01NS038631

Revision History 

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-03-21
    Type: Database references
  • Version 1.2: 2018-03-28
    Type: Data collection, Database references
  • Version 1.3: 2019-02-20
    Type: Author supporting evidence, Data collection