9BQI

Cryo-EM structure of BAY-1797 bound to the full-length human P2X4 receptor in the closed state

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-05-09 Released: 2025-01-29 
  • Deposition Author(s): Shi, H., Ditter, I.A., Oken, A.C., Mansoor, S.E.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.55 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

Human P2X4 receptor gating is modulated by a stable cytoplasmic cap and a unique allosteric pocket.

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

(2025) Sci Adv 11: eadr3315-eadr3315

  • DOI: https://doi.org/10.1126/sciadv.adr3315
  • Primary Citation of Related Structures:  
    9BQH, 9BQI, 9C48

  • PubMed Abstract: 

    P2X receptors (P2XRs) are adenosine 5'-triphosphate (ATP)-gated ion channels comprising homomeric and heteromeric trimers of seven subtypes (P2X1-P2X7) that confer different rates of desensitization. The helical recoil model of P2XR desensitization proposes stability of the cytoplasmic cap sets the rate of desensitization, but timing of its formation is unclear for slow-desensitizing P2XRs. We report cryo-electron microscopy structures of full-length wild-type human P2X4 receptor in apo closed, antagonist-bound inhibited, and ATP-bound desensitized states. Because the apo closed and antagonist-bound inhibited state structures of this slow-desensitizing P2XR include an intact cytoplasmic cap while the ATP-bound desensitized state structure does not, the cytoplasmic cap is formed before agonist binding. Furthermore, structural and functional data suggest the cytoplasmic cap is stabilized by lipids to modulate desensitization, and P2X4 is modified by glycosylation and palmitoylation. Last, our antagonist-bound inhibited state structure reveals features specific to the allosteric ligand-binding pocket in human receptors that facilitates development of small-molecule modulators.


  • 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 4A,
B [auth C],
C [auth B]
388Homo sapiensMutation(s): 0 
Gene Names: P2RX4
UniProt & NIH Common Fund Data Resources
Find proteins for Q99571 (Homo sapiens)
Explore Q99571 
Go to UniProtKB:  Q99571
PHAROS:  Q99571
GTEx:  ENSG00000135124 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99571
Glycosylation
Glycosylation Sites: 4Go to GlyGen: Q99571-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E, G, H, J
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
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
F, I, L
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMT (Subject of Investigation/LOI)
Query on LMT

Download Ideal Coordinates CCD File 
O [auth A]
P [auth A]
Q [auth C]
T [auth C]
U [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
P6E (Subject of Investigation/LOI)
Query on P6E

Download Ideal Coordinates CCD File 
N [auth A],
R [auth C],
W [auth B]
N-[4-(3-chloranylphenoxy)-3-sulfamoyl-phenyl]-2-phenyl-ethanamide
C20 H17 Cl N2 O4 S
CSJYMAFXYMYNCK-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
M [auth A],
S [auth C],
X [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.55 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: 2025-01-29
    Type: Initial release