9BQI | pdb_00009bqi

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9BQI

This is version 1.1 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 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.

Macromolecule Content 

  • Total Structure Weight: 139.53 kDa 
  • Atom Count: 9,552 
  • Modeled Residue Count: 1,122 
  • Deposited Residue Count: 1,164 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
P2X purinoceptor 4A,
B [auth C],
C [auth B]
388Homo sapiensMutation(s): 0 
Gene Names: P2RX4
Membrane Entity: Yes 
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 GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E, G, H, J
D, E, G, H, J, K
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD 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]
O [auth A],
P [auth A],
Q [auth C],
T [auth C],
U [auth B],
V [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 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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
  • Version 1.1: 2025-05-14
    Changes: Data collection