9B95

Cryo-EM structure of the closed NF449-bound human P2X1 receptor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.61 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into the human P2X1 receptor and ligand interactions.

Bennetts, F.M.Venugopal, H.Glukhova, A.Mobbs, J.I.Ventura, S.Thal, D.M.

(2024) Nat Commun 15: 8418-8418

  • DOI: https://doi.org/10.1038/s41467-024-52776-7
  • Primary Citation of Related Structures:  
    9B73, 9B95

  • PubMed Abstract: 

    The P2X1 receptor is a trimeric ligand-gated ion channel that plays an important role in urogenital and immune functions, offering the potential for new drug treatments. However, progress in this area has been hindered by limited structural information and a lack of well-characterised tool compounds. In this study, we employ cryogenic electron microscopy (cryo-EM) to elucidate the structures of the P2X1 receptor in an ATP-bound desensitised state and an NF449-bound closed state. NF449, a potent P2X1 receptor antagonist, engages the receptor distinctively, while ATP, the endogenous ligand, binds in a manner consistent with other P2X receptors. To explore the molecular basis of receptor inhibition, activation, and ligand interactions, key residues involved in ligand and metal ion binding were mutated. Radioligand binding assays with [ 3 H]-α,β-methylene ATP and intracellular calcium ion influx assays were used to evaluate the effects of these mutations. These experiments validate key ligand-receptor interactions and identify conserved and non-conserved residues critical for ligand binding or receptor modulation. This research expands our understanding of the P2X1 receptor structure at a molecular level and opens new avenues for in silico drug design targeting the P2X1 receptor.


  • Organizational Affiliation

    Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
P2X purinoceptor 1
A, B, C
399Homo sapiensMutation(s): 0 
Gene Names: P2RX1P2X1
UniProt & NIH Common Fund Data Resources
Find proteins for P51575 (Homo sapiens)
Explore P51575 
Go to UniProtKB:  P51575
PHAROS:  P51575
GTEx:  ENSG00000108405 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51575
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P51575-1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.61 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1
RECONSTRUCTIONcryoSPARC1.4

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1196951

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection