3I5D

Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at 3.5 Angstroms (R3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.46 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.276 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the ATP-gated P2X(4) ion channel in the closed state.

Kawate, T.Michel, J.C.Birdsong, W.T.Gouaux, E.

(2009) Nature 460: 592-598

  • DOI: 10.1038/nature08198
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • P2X receptors are cation-selective ion channels gated by extracellular ATP, and are implicated in diverse physiological processes, from synaptic transmission to inflammation to the sensing of taste and pain. Because P2X receptors are not related to o ...

    P2X receptors are cation-selective ion channels gated by extracellular ATP, and are implicated in diverse physiological processes, from synaptic transmission to inflammation to the sensing of taste and pain. Because P2X receptors are not related to other ion channel proteins of known structure, there is at present no molecular foundation for mechanisms of ligand-gating, allosteric modulation and ion permeation. Here we present crystal structures of the zebrafish P2X(4) receptor in its closed, resting state. The chalice-shaped, trimeric receptor is knit together by subunit-subunit contacts implicated in ion channel gating and receptor assembly. Extracellular domains, rich in beta-strands, have large acidic patches that may attract cations, through fenestrations, to vestibules near the ion channel. In the transmembrane pore, the 'gate' is defined by an approximately 8 A slab of protein. We define the location of three non-canonical, intersubunit ATP-binding sites, and suggest that ATP binding promotes subunit rearrangement and ion channel opening.


    Organizational Affiliation

    Vollum Institute, Oregon Health and Science University, 3181 Southwest Sam Jackson Park Road, Oregon 97239, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
P2X purinoceptor
A, B, C
356Danio rerioMutation(s): 1 
Gene Names: p2rx4a
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
ATP-gated P2X4 ion channel (apo protein; ΔP2X4-B construct)
Find proteins for Q6NYR1 (Danio rerio)
Go to UniProtKB:  Q6NYR1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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: 3.46 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.276 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 234.910α = 90.00
b = 234.910β = 90.00
c = 138.433γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHENIXrefinement
SCALEPACKdata scaling
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description