5WKY

Bromide sites in the structure of an acid sensing ion channel in a resting state

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

  • Deposited: 2017-07-25 Released: 2018-08-08 
  • 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: 4 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.281 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Divalent cation and chloride ion sites of chicken acid sensing ion channel 1a elucidated by x-ray crystallography.

Yoder, N.Gouaux, E.

(2018) PLoS ONE 13: e0202134-e0202134

  • DOI: 10.1371/journal.pone.0202134
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Acid sensing ion channels (ASICs) are proton-gated ion channels that are members of the degenerin/epithelial sodium channel superfamily and are expressed throughout central and peripheral nervous systems. ASICs have been implicated in multiple physio ...

    Acid sensing ion channels (ASICs) are proton-gated ion channels that are members of the degenerin/epithelial sodium channel superfamily and are expressed throughout central and peripheral nervous systems. ASICs have been implicated in multiple physiological processes and are subject to numerous forms of endogenous and exogenous regulation that include modulation by Ca2+ and Cl- ions. However, the mapping of ion binding sites as well as a structure-based understanding of the mechanisms underlying ionic modulation of ASICs have remained elusive. Here we present ion binding sites of chicken ASIC1a in resting and desensitized states at high and low pH, respectively, determined by anomalous diffraction x-ray crystallography. The acidic pocket serves as a nexus for divalent cation binding at both low and high pH, while we observe divalent cation binding within the central vestibule on the resting channel at high pH only. Moreover, neutralization of residues positioned to coordinate divalent cations via individual and combined Glu to Gln substitutions reduced, but did not extinguish, modulation of proton-dependent gating by Ca2+. Additionally, we demonstrate that anion binding at the canonical thumb domain site is state-dependent and present a previously undetected anion site at the mouth of the extracellular fenestrations on the resting channel. Our results map anion and cation sites on ASICs across multiple functional states, informing possible mechanisms of modulation and providing a blueprint for the design of therapeutics targeting ASICs.


    Organizational Affiliation

    Vollum Institute, Oregon Health & Science University, Portland, Oregon, United States of America.




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)
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, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
BA
Query on BA

Download SDF File 
Download CCD File 
A
BARIUM ION
Ba
XDFCIPNJCBUZJN-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: 4 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.281 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 109.550α = 90.00
b = 134.490β = 90.00
c = 159.130γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHENIXphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-07-25 
  • Released Date: 2018-08-08 
  • 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: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-09-19
    Type: Data collection, Database references
  • Version 1.2: 2019-02-20
    Type: Author supporting evidence, Data collection
  • Version 1.3: 2019-04-17
    Type: Author supporting evidence, Data collection