9S3O | pdb_00009s3o

Cerebellar GluA2/4 NTD heterophilic tetramer interface (focused refinement)

• PDB DOI: https://doi.org/10.2210/pdb9S3O/pdb
• EM Map EMD-54543: EMDB EMDataResource

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


• Deposited: 2025-07-24 Released: 2025-12-24 
• Deposition Author(s): Sengupta, N., Scrutton, A., Greger, I.H., Krieger, J.M.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom), Wellcome Trust

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 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 post-transcriptional modifications. Here, using mass-spectrometry, cryo-EM, and electrophysiology, we characterize major cerebellar AMPARs in pig: calcium-impermeable GluA2/A4 heteromers with four TARP subunits, mainly neuronal in origin, and BG-specific calcium-permeable GluA1/A4 heteromers containing two Type-2 TARPs. We also showed that GluA4 receptors consistently 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.

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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, Japan.F.
PNAC Division, Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 189.52 kDa 
• Atom Count: 5,384 
• Modeled Residue Count: 700 
• Deposited Residue Count: 1,685 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor 4	A [auth B]	863	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for I3L8N9 (Sus scrofa) Explore I3L8N9  Go to UniProtKB:  I3L8N9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor 2	B [auth D]	822	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A5G2QRQ2 (Sus scrofa) Explore A0A5G2QRQ2  Go to UniProtKB:  A0A5G2QRQ2
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	C [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Sengupta, N., Scrutton, A., Greger, I.H., Krieger, J.M.

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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: 2025-12-24
  Type: Initial release
  
• Version 1.1: 2026-04-08
  Changes: Data collection, Database references