5U1U | pdb_00005u1u

Crystal structure of the ATP-gated P2X7 ion channel bound to allosteric antagonist A740003

• PDB DOI: https://doi.org/10.2210/pdb5U1U/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Ailuropoda melanoleuca
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTM


• Deposited: 2016-11-29 Released: 2017-01-11 
• Deposition Author(s): Karasawa, A., Kawate, T.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 
  0.261 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Structural basis for subtype-specific inhibition of the P2X7 receptor.

Karasawa, A., Kawate, T.

(2016) Elife 5

• PubMed: 27935479 
• DOI: https://doi.org/10.7554/eLife.22153
• Primary Citation Related Structures: 
  5U1L, 5U1U, 5U1V, 5U1W, 5U1X, 5U1Y, 5U2H


• PubMed Abstract: 
  

  The P2X7 receptor is a non-selective cation channel activated by extracellular adenosine triphosphate (ATP). Chronic activation of P2X7 underlies many health problems such as pathologic pain, yet we lack effective antagonists due to poorly understood mechanisms of inhibition. Here we present crystal structures of a mammalian P2X7 receptor complexed with five structurally-unrelated antagonists. Unexpectedly, these drugs all bind to an allosteric site distinct from the ATP-binding pocket in a groove formed between two neighboring subunits. This novel drug-binding pocket accommodates a diversity of small molecules mainly through hydrophobic interactions. Functional assays propose that these compounds allosterically prevent narrowing of the drug-binding pocket and the turret-like architecture during channel opening, which is consistent with a site of action distal to the ATP-binding pocket. These novel mechanistic insights will facilitate the development of P2X7-specific drugs for treating human diseases.

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Organizational Affiliation: 
• Department of Molecular Medicine, Cornell University, Ithaca, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.85 kDa 
• Atom Count: 2,384 
• Modeled Residue Count: 314 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P2X purinoceptor	A	342	Ailuropoda melanoleuca	Mutation(s): 5  Gene Names: P2RX7 Membrane Entity: Yes
UniProt
Find proteins for G1M6C4 (Ailuropoda melanoleuca) Explore G1M6C4  Go to UniProtKB:  G1M6C4
Glycosylation
Glycosylation Sites: 3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7S4	E [auth A]	N-{(1R)-1-[N''-cyano-N'-(quinolin-5-yl)carbamimidamido]-2,2-dimethylpropyl}-2-(3,4-dimethoxyphenyl)acetamide C26 H30 N6 O3 PUHSRMSFDASMAE-DEOSSOPVSA-N
NAG	B [auth A], C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free:  0.261 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.566	α = 90
b = 169.566	β = 90
c = 169.566	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-01-11 
Deposition Author(s): Karasawa, A., Kawate, T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM114379
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	NS072869

Revision History  

• Version 1.0: 2017-01-11
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Refinement description
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.5: 2024-10-23
  Changes: Structure summary