9DDV | pdb_00009ddv

Cryo-EM structure of the human P2X2 receptor in the apo closed state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Subtype-specific structural features of the hearing loss-associated human P2X2 receptor.

Westermann, F.G.Oken, A.C.Granith, P.K.E.Marimuthu, P.Muller, C.E.Mansoor, S.E.

(2025) Proc Natl Acad Sci U S A 122: e2417753122-e2417753122

  • DOI: https://doi.org/10.1073/pnas.2417753122
  • Primary Citation of Related Structures:  
    9DDV, 9DDW, 9DDX

  • PubMed Abstract: 

    The P2X2 receptor (P2X2R) is a slowly desensitizing adenosine triphosphate (ATP)-gated ion channel that is highly expressed in the cochlea. When mutated, the P2X2R exacerbates age- and noise-related hearing loss, but selective modulators of the receptor are lacking, and the molecular basis of activation and desensitization remains poorly understood. Here, we determine high-resolution cryoelectron microscopy structures of the full-length wild-type human P2X2R in an apo closed state and two distinct ATP-bound desensitized states. In the apo closed state structure, we observe features unique to the P2X2R and locate disease mutations within or near the transmembrane domain. In addition, our ATP-bound structures show how free anionic ATP forms subtype-specific interactions with the orthosteric binding site. We identify and characterize two different ATP-bound desensitized state structures, one similar to published models for other P2XR subtypes, and a second alternate conformation not previously observed. A loop adjacent to the orthosteric binding site between these two ATP-bound desensitized state structures undergoes significant conformational changes. These movements are supported by multireplicate, microsecond-scale molecular dynamics simulation studies and suggest a path by which ATP could enter or leave the orthosteric pocket. Together, our results provide structural insights into the P2X2R, facilitating structure-based drug development for this therapeutically important target.


  • Organizational Affiliation
    • PharmaCenter Bonn and Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn 53121, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
P2X purinoceptor 2
A, B, C
471Homo sapiensMutation(s): 0 
Gene Names: P2RX2P2X2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBL9 (Homo sapiens)
Explore Q9UBL9 
Go to UniProtKB:  Q9UBL9
PHAROS:  Q9UBL9
GTEx:  ENSG00000187848 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBL9
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q9UBL9-1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR00HL138129
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesDP2GM149551

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-24
    Type: Initial release