5XW6

Crystal structure of the chicken ATP-gated P2X7 receptor channel in the presence of competitive antagonist TNP-ATP at 3.1 Angstroms

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Gallus gallus
  • Expression System: Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2017-06-29 Released: 2017-10-25 
  • Deposition Author(s): Kasuya, G., Hattori, M., Nureki, O.
  • Funding Organization(s): Japan Society for the Promotion of Science, the Ministry of Science and Technology of China, the National Natural Science Foundation of China

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 

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This is version 1.2 of the entry. See complete history


Literature

Structural insights into the competitive inhibition of the ATP-gated P2X receptor channel

Kasuya, G.Yamaura, T.Ma, X.B.Nakamura, R.Takemoto, M.Nagumo, H.Tanaka, E.Dohmae, N.Nakane, T.Yu, Y.Ishitani, R.Matsuzaki, O.Hattori, M.Nureki, O.

(2017) Nat Commun 8: 876-876

  • DOI: https://doi.org/10.1038/s41467-017-00887-9
  • Primary Citation of Related Structures:  
    5XW6

  • PubMed Abstract: 

    P2X receptors are non-selective cation channels gated by extracellular ATP, and the P2X7 receptor subtype plays a crucial role in the immune and nervous systems. Altered expression and dysfunctions of P2X7 receptors caused by genetic deletions, mutations, and polymorphic variations have been linked to various diseases, such as rheumatoid arthritis and hypertension. Despite the availability of crystal structures of P2X receptors, the mechanism of competitive antagonist action for P2X receptors remains controversial. Here, we determine the crystal structure of the chicken P2X7 receptor in complex with the competitive P2X antagonist, TNP-ATP. The structure reveals an expanded, incompletely activated conformation of the channel, and identified the unique recognition manner of TNP-ATP, which is distinct from that observed in the previously determined human P2X3 receptor structure. A structure-based computational analysis furnishes mechanistic insights into the TNP-ATP-dependent inhibition. Our work provides structural insights into the functional mechanism of the P2X competitive antagonist.P2X receptors are nonselective cation channels that are gated by extracellular ATP. Here the authors present the crystal structure of chicken P2X7 with its bound competitive antagonist TNP-ATP and give mechanistic insights into TNP-ATP dependent inhibition through further computational analysis and electrophysiology measurements.


  • Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
P2X purinoceptorA [auth C],
B [auth A],
C [auth B]
327Gallus gallusMutation(s): 1 
Gene Names: P2RX7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.038α = 90
b = 113.038β = 90
c = 333.472γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan16H06294
Japan Society for the Promotion of ScienceJapan24227004
the Ministry of Science and Technology of ChinaChina2016YFA0502800
the National Natural Science Foundation of ChinaChina31570838
the National Natural Science Foundation of ChinaChina31650110469

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description, Structure summary