9P9E | pdb_00009p9e

Active substate 3 of the GluA4 homotetramer.

• PDB DOI: https://doi.org/10.2210/pdb9P9E/pdb
• EM Map EMD-71408: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Rattus norvegicus, Mus musculus
• Expression System: Mus musculus, Homo sapiens
• Mutation(s): No 


• Deposited: 2025-06-24 Released: 2026-01-28 
• Deposition Author(s): Hale, W.D., Huganir, R.L., Twomey, E.C.
• Funding Organization(s): National Institutes of Health/National Institute of Mental Health (NIH/NIMH), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.82 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for activation and conformational plasticity of the GluA4 AMPA receptor.

Hale, W.D., Wang, H., Huganir, R.L., Twomey, E.C.

(2026) Nat Commun 17

• PubMed: 41656278 
• DOI: https://doi.org/10.1038/s41467-026-68953-9
• Primary Citation Related Structures: 
  9P9B, 9P9C, 9P9D, 9P9E, 9P9F, 9P9G


• PubMed Abstract: 
  

  AMPA-subtype glutamate receptors (AMPARs) mediate excitatory synaptic transmission. AMPAR ion channels exhibit multiple subconductance states that tune neuronal responses to glutamate. GluA4 is the rarest subunit in the brain but is enriched in interneurons and the cerebellum. Rising evidence points to GluA4 AMPARs in the development of neurological diseases, but the structural mechanisms of GluA4 function remain enigmatic. Here, we show the distinct features of GluA4 that tune AMPAR function. We find that GluA4 AMPARs have a canonical "Y" shaped architecture where local dimer pairs are domain-swapped between the amino terminal domain (NTD) and ligand binding domain (LBD), both of which comprise the extracellular domain. All four LBDs are glutamate bound yet open the GluA4 ion channel by asymmetric hinging in all four channel helices. We observe that the glutamate-saturated LBD has conformational plasticity, which tunes the ion channel gate below. These data provide a framework for understanding channel subconductance, outline the distinct properties of GluA4, expand our understanding of conformational plasticity in AMPARs, and will inform therapeutic design.

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Organizational Affiliation: 
• Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA. [e-mail].
Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. [e-mail].
Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA. [e-mail].
Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA. [e-mail].
The Beckman Center for Cryo-EM at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD, USA. [e-mail].
Diana Helis Henry Medical Research Foundation, New Orleans, LA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 474.97 kDa 
• Atom Count: 18,100 
• Modeled Residue Count: 2,304 
• Deposited Residue Count: 4,220 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Glutamate receptor 4	A, B, C, D	846	Rattus norvegicus	Mutation(s): 0  Gene Names: Gria4, Glur4
UniProt
Find proteins for P19493 (Rattus norvegicus) Explore P19493  Go to UniProtKB:  P19493

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent calcium channel gamma-2 subunit	E [auth H], F, G, H [auth E]	209	Mus musculus	Mutation(s): 0  Gene Names: Cacng2, Stg
UniProt & NIH Common Fund Data Resources
Find proteins for O88602 (Mus musculus) Explore O88602  Go to UniProtKB:  O88602
IMPC:  MGI:1316660

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYZ	J [auth A], L [auth B], M [auth B], P [auth D]	CYCLOTHIAZIDE C14 H16 Cl N3 O4 S2 BOCUKUHCLICSIY-KSCJFIISSA-N
GLU	I [auth A], K [auth B], N [auth C], O [auth D]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CYZ	BindingDB:  9P9E	EC50: 3800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.82 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-01-28 
Deposition Author(s): Hale, W.D., Huganir, R.L., Twomey, E.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	K99MH132811
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R37NS036715
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM154904

Revision History  

• Version 1.0: 2026-01-28
  Type: Initial release
  
• Version 1.1: 2026-09-23
  Changes: Data collection, Database references