9S3Z | pdb_00009s3z

Cerebellar GluA1/4 LBD tetramer (focused refinement)

• PDB DOI: https://doi.org/10.2210/pdb9S3Z/pdb
• EM Map EMD-54556: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2025-07-25 Released: 2025-12-31 
• Deposition Author(s): Sengupta, N., Scrutton, A., Greger, I.H., Krieger, J.M.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom), Wellcome Trust

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.55 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico

Literature

Structure and organization of AMPA receptor-TARP complexes in the mammalian cerebellum.

Scrutton, A.M., Sengupta, N., Ivica, J., Stockwell, I., Peak-Chew, S., Singh, B., Suzuki, K., Chang, V.T., McLaughlin, S.H., Krieger, J.M., Aricescu, A.R., Greger, I.H.

(2026) Science 391: 1361-1367

• PubMed: 41379938 
• DOI: https://doi.org/10.1126/science.aeb3577
• Primary Citation Related Structures: 
  9S3O, 9S3Q, 9S3Z, 9S41


• PubMed Abstract: 
  

  AMPA receptors (AMPARs) are multimodal transducers of glutamatergic signals throughout the brain. Their diversity is exemplified in the cerebellum: At afferent synapses, AMPARs mediate high-frequency excitation, whereas in Bergmann glia (BG) they support calcium transients that modulate synaptic transmission. This spectrum arises from different combinations of core subunits (GluA1-4), auxiliary proteins, and posttranscriptional modifications. Using mass spectrometry, cryo-electron microscopy, and electrophysiology, we characterize major cerebellar AMPARs in pigs: calcium-impermeable GluA2/A4 heteromers with four transmembrane AMPAR regulatory protein (TARP) subunits, mainly neuronal in origin, and BG-specific, calcium-permeable GluA1/A4 heteromers containing two type II TARPs. We also showed that GluA4 receptors frequently exhibit compact N-terminal domains that promote their synaptic delivery. Our study defines the organizational principles of mammalian cerebellar AMPAR complexes and reveals how different receptor subtypes support cell type-specific functions.

---

Organizational Affiliation: 
• Neurobiology Division, Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK.
Cell Biology Division, Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK.
Department of Genomic Medicine; University of Texas MD Anderson Cancer Center Houston, TX, USA.
Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan.
PNAC Division, Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 394.86 kDa 
• Atom Count: 8,355 
• Modeled Residue Count: 1,087 
• Deposited Residue Count: 3,502 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor 1	A, C	888	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A286ZS63 (Sus scrofa) Explore A0A286ZS63  Go to UniProtKB:  A0A286ZS63

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor 4	B, D	863	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for I3L8N9 (Sus scrofa) Explore I3L8N9  Go to UniProtKB:  I3L8N9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E2Q (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide C12 H8 N4 O6 S UQNAFPHGVPVTAL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.55 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot
MODEL REFINEMENT	REFMAC
MODEL REFINEMENT	ISOLDE

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-31 
Deposition Author(s): Sengupta, N., Scrutton, A., Greger, I.H., Krieger, J.M.

---

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_U105174197
Wellcome Trust	United Kingdom	223194/Z/21/Z

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release
  
• Version 1.1: 2026-04-08
  Changes: Data collection, Database references