9GP7 | pdb_00009gp7

Cryo EM structure of the E307T mutant of the human P2X4 receptor in complex with the anthraquinone derivative PSB-0704

• PDB DOI: https://doi.org/10.2210/pdb9GP7/pdb
• EM Map EMD-51502: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2024-09-06 Released: 2025-11-26 
• Deposition Author(s): Nagel, J., Vaaen, V., Torp, J., Geyer, M., Claff, T., Hagelueken, G., Mueller, C.E.
• Funding Organization(s): German Research Foundation (DFG), German Federal Ministry for Education and Research, European Cooperation in Science and Technology (COST) action

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.35 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Discovery of an allosteric P2X receptor binding site for anthraquinones by a chimeric approach combined with computational studies, bump-and-hole mutagenesis, and cryo-electron microscopy

Nagel, J., Weinhausen, S., Namasivayam, V., Baqi, Y., Al Musawi, H.A.M., Abdelrahman, A., Vaassen, V., Schlegel, J., Taplick, L., Torp, J., Kubicek, J., Maertens, B., Geyer, M., Claff, T., Hagelueken, G., Mueller, C.E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 142.33 kDa 
• Atom Count: 7,338 
• Modeled Residue Count: 909 
• Deposited Residue Count: 1,236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P2X purinoceptor 4	A, B, C	412	Homo sapiens	Mutation(s): 3  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
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q99571-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, F	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1INJ (Subject of Investigation/LOI)	G [auth A], I [auth A], K [auth C]	1-azanyl-4-[(3-carboxy-4-phenylazanyl-phenyl)amino]-9,10-bis(oxidanylidene)anthracene-2-carboxylic acid C28 H19 N3 O6 ZHWHOYJCXUJFDK-UHFFFAOYSA-N
NAG	H [auth A], J [auth B], L [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.35 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Nagel, J., Vaaen, V., Torp, J., Geyer, M., Claff, T., Hagelueken, G., Mueller, C.E.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB 1328
German Federal Ministry for Education and Research	Germany	0315606B
European Cooperation in Science and Technology (COST) action	European Union	CA21130

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release