5SVM

Crystal structure of the ATP-gated human P2X3 ion channel bound to agonist 2-methylthio-ATP in the desensitized state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.093 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-ray structures define human P2X3 receptor gating cycle and antagonist action.

Mansoor, S.E.Lu, W.Oosterheert, W.Shekhar, M.Tajkhorshid, E.Gouaux, E.

(2016) Nature 538: 66-71

  • DOI: 10.1038/nature19367
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • P2X receptors are trimeric, non-selective cation channels activated by ATP that have important roles in the cardiovascular, neuronal and immune systems. Despite their central function in human physiology and although they are potential targets of the ...

    P2X receptors are trimeric, non-selective cation channels activated by ATP that have important roles in the cardiovascular, neuronal and immune systems. Despite their central function in human physiology and although they are potential targets of therapeutic agents, there are no structures of human P2X receptors. The mechanisms of receptor desensitization and ion permeation, principles of antagonism, and complete structures of the pore-forming transmembrane domains of these receptors remain unclear. Here we report X-ray crystal structures of the human P2X3 receptor in apo/resting, agonist-bound/open-pore, agonist-bound/closed-pore/desensitized and antagonist-bound/closed states. The open state structure harbours an intracellular motif we term the 'cytoplasmic cap', which stabilizes the open state of the ion channel pore and creates lateral, phospholipid-lined cytoplasmic fenestrations for water and ion egress. The competitive antagonists TNP-ATP and A-317491 stabilize the apo/resting state and reveal the interactions responsible for competitive inhibition. These structures illuminate the conformational rearrangements that underlie P2X receptor gating and provide a foundation for the development of new pharmacological agents.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
P2X purinoceptor 3
A, B
363Homo sapiensMutation(s): 0 
Gene Names: P2RX3
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
ATP-gated P2X3 ion channel, closed apo state
Find proteins for P56373 (Homo sapiens)
Go to Gene View: P2RX3
Go to UniProtKB:  P56373
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
6AT
Query on 6AT

Download SDF File 
Download CCD File 
A
2-(methylsulfanyl)adenosine 5'-(tetrahydrogen triphosphate)
2-methylthio-adenosine-5'-triphosphate
C11 H18 N5 O13 P3 S
XNOBOKJVOTYSJV-KQYNXXCUSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-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
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ATPEC50: 340 nM (99) BINDINGDB
6ATKi: 8.2 nM (99) BINDINGDB
6ATEC50: 350 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.093 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.203 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 172.640α = 90.00
b = 172.640β = 90.00
c = 172.640γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2016-10-19
    Type: Database references