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Structure paper

TitleStructural basis for a central permeation pathway in the P2X1 receptor.
Journal, issue, pagesCell Discov, Vol. 12, Issue 1, Year 2026
Publish dateJun 4, 2026
AuthorsHeng Zhang / Pengpeng Wu / Zhiyong Gu / Youwei Xu / Wen Hu / Qingning Yuan / Bingqing Xia / H Eric Xu / Zhaobing Gao /
PubMed AbstractThe ion permeation pathway is a critical determinant of ion channel function and selectivity; however, the structural basis for ion permeation in the P2X1 receptor, an ATP-gated ion channel crucial ...The ion permeation pathway is a critical determinant of ion channel function and selectivity; however, the structural basis for ion permeation in the P2X1 receptor, an ATP-gated ion channel crucial for platelet activation, thrombosis, and male infertility, remains incompletely understood. Here, we present high-resolution cryo-electron microscopy (cryo-EM) structures of the P2X1 receptor, which reveal a central ion permeation pathway spanning the entire extracellular domain, complementing the existing paradigms of ion channel architecture for the P2X receptor family. Within this pathway, we identify specific sites that coordinate hydrated calcium ions, including an aspartate ring that acts as a selectivity filter at the apex of the central vestibule. We also discover that a small molecule, 3,5-bis(trifluoromethyl)aniline, binds at the top of the central vestibule and potently inhibits cation flux through this central permeation pathway. Our findings reveal a new inhibitor-binding site in the P2X1 receptor. These insights provide a structural framework for the rational design of subtype-specific P2X receptor inhibitors targeting the central vestibule.
External linksCell Discov / PubMed:42243080 / PubMed Central
MethodsEM (single particle)
Resolution2.31 - 3.14 Å
Structure data

60438

8zt1

EMDB-60438, PDB-8zt1:
sStructure of calcium preference ATP-gated channel P2X1 in complex with BTFA
Method: EM (single particle) / Resolution: 2.8 Å

60445

8zt2

EMDB-60445, PDB-8zt2:
Structure of calcium preference ATP-gated channel Apo-P2X1 in the Desensitized state 1
Method: EM (single particle) / Resolution: 2.31 Å

60447

8zt5

EMDB-60447, PDB-8zt5:
Structure of calcium preference ATP-gated channel P2X1 in the Desensitized state 2 in the presence of 1mM Calcium ion
Method: EM (single particle) / Resolution: 2.35 Å

60453

8zt8

EMDB-60453, PDB-8zt8:
Structure of calcium preference ATP-gated channel P2X1 in the Desensitized state 3 in the presence of 5mM Calcium ion
Method: EM (single particle) / Resolution: 2.34 Å

60457

8zta

EMDB-60457, PDB-8zta:
Structure of calcium preference ATP-gated channel P2X1 in the Desensitized state 4 in the presence of 10mM Calcium ion
Method: EM (single particle) / Resolution: 2.58 Å

60458

8ztd

EMDB-60458, PDB-8ztd:
Structure of calcium preference ATP-gated channel P2X1 in the Desensitized state 5 in the presence of 10 mM Calcium ion
Method: EM (single particle) / Resolution: 2.63 Å

60460

8ztf

EMDB-60460, PDB-8ztf:
Structure of calcium preference ATP-gated channel P2X1 in the Pre-open state in the presence of 10mM Calcium ion
Method: EM (single particle) / Resolution: 2.43 Å

67120

9xqr

EMDB-67120, PDB-9xqr:
Cryo-EM structure of P1X1 in complex with BTFA
Method: EM (single particle) / Resolution: 3.14 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

PDB-1d8z:
SOLUTION STRUCTURE OF THE FIRST RNA-BINDING DOMAIN (RBD1) OF HU ANTIGEN C (HUC)

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-CA:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER

Source
  • mus musculus (house mouse)
KeywordsTRANSPORT PROTEIN / ion channel / MEMBRANE PROTEIN

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