9C2B

Cryo-EM structure of the human P2X1 receptor in the ATP-bound desensitized state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.42 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

Cryo-EM structures of the human P2X1 receptor reveal subtype-specific architecture and antagonism by supramolecular ligand-binding.

Oken, A.C.Lisi, N.E.Ditter, I.A.Shi, H.Nechiporuk, N.A.Mansoor, S.E.

(2024) Nat Commun 15: 8490-8490

  • DOI: https://doi.org/10.1038/s41467-024-52636-4
  • Primary Citation of Related Structures:  
    9C2A, 9C2B, 9C2C

  • PubMed Abstract: 

    P2X receptors are a family of seven trimeric non-selective cation channels that are activated by extracellular ATP to play roles in the cardiovascular, neuronal, and immune systems. Although it is known that the P2X1 receptor subtype has increased sensitivity to ATP and fast desensitization kinetics, an underlying molecular explanation for these subtype-selective features is lacking. Here we report high-resolution cryo-EM structures of the human P2X1 receptor in the apo closed, ATP-bound desensitized, and the high-affinity antagonist NF449-bound inhibited states. The apo closed and ATP-bound desensitized state structures of human P2X1 define subtype-specific properties such as distinct pore architecture and ATP-interacting residues. The NF449-bound inhibited state structure of human P2X1 reveals that NF449 has a unique dual-ligand supramolecular binding mode at the interface of neighboring protomers, inhibiting channel activation by overlapping with the canonical P2X receptor ATP-binding site. Altogether, these data define the molecular pharmacology of the human P2X1 receptor laying the foundation for structure-based drug design.


  • Organizational Affiliation

    Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR, 97239, USA.


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: 3Go to GlyGen: P51575-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, F, H
3N-Glycosylation
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, G, I
2N-Glycosylation
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
L [auth A],
O [auth B],
P [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
K [auth A],
N [auth B],
R [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
J [auth A],
M [auth B],
Q [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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: 2024-10-09
    Type: Initial release