9J8K | pdb_00009j8k

Crystal structure of the GluA2 ligand binding core (S1S2J) in complex with fluorophore-ligand conjugate

• PDB DOI: https://doi.org/10.2210/pdb9J8K/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-21 Released: 2025-07-02 
• Deposition Author(s): Fujiwara, T., Adriel, H., Soga, K., Kiyonaka, S., Nango, E.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.200 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Rapid and reversible fluorescent probe enables repeated snapshot imaging of AMPA receptors during synaptic plasticity.

Soga, K., Fujiwara, T., Nakagawa, M., Shibata, A., Adriel, H., Yatsuzuka, K., Kakegawa, W., Yuzaki, M., Hamachi, I., Nango, E., Kiyonaka, S.

(2025) Sci Adv 11: eadt6683-eadt6683

• PubMed: 40479050 
• DOI: https://doi.org/10.1126/sciadv.adt6683
• Primary Citation Related Structures: 
  9J8K


• PubMed Abstract: 
  

  The subcellular localization of neurotransmitter receptors is strictly regulated in neurons. Changes in the trafficking of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type glutamate receptors (AMPARs) play an essential role in synaptic plasticity, which is the cellular basis of learning and memory. To explore receptor trafficking, genetically encoded approaches (e.g., the fusion of fluorescent proteins to receptors) are often used. However, concerns remain that genetic approaches cannot fully reproduce the receptor functions that are inherent to neurons. Herein, we report on PFQX1(AF488), a fluorescent probe for the visualization of cell-surface AMPARs without any genetic manipulation to neurons. The rapid and reversible staining features of this probe enabled snapshot imaging, which showed the accumulation of native AMPARs in dendritic spines during synaptic plasticity. Moreover, the mechanism of this synaptic accumulation, for which genetically encoded approaches have given controversial results, was revealed by integrating two chemical methods: PFQX1(AF488) and covalent chemical labeling.

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Organizational Affiliation: 
• Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Aichi 464-8603, Japan.
Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi 980-8577, Japan.
Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi 980-8578, Japan.
Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan.
Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan.
RIKEN SPring-8 Center, Sayo, Hyogo 679-5198, Japan.
Research Institute for Quantum and Chemical Innovation, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Aichi 464-8603, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 31.43 kDa 
• Atom Count: 2,363 
• Modeled Residue Count: 259 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GluA2 ligand binding core	A	272	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P19491 (Rattus norvegicus) Explore P19491  Go to UniProtKB:  P19491

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L33 (Subject of Investigation/LOI)	B [auth A]	2-(3-azanyl-6-azanylidene-4,5-disulfo-xanthen-9-yl)-5-[[1-[4-(2-hydroxy-2-oxoethyl)-2,3-bis(oxidanylidene)-7-(trifluoromethyl)-1~{H}-quinoxalin-6-yl]pyrrol-3-yl]methylcarbamoyl]benzoic acid C37 H25 F3 N6 O14 S2 WYMZJRUHFVFSCC-YTJQMYRNSA-N
PEG	E [auth A], F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.200 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.94	α = 90
b = 69.94	β = 90
c = 227.52	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Fujiwara, T., Adriel, H., Soga, K., Kiyonaka, S., Nango, E.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	19H05781
Japan Society for the Promotion of Science (JSPS)	Japan	24H00547
Japan Society for the Promotion of Science (JSPS)	Japan	24H02262

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release