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- PDB-9s3z: Cerebellar GluA1/4 LBD tetramer (focused refinement) -

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Basic information

Entry
Database: PDB / ID: 9s3z
TitleCerebellar GluA1/4 LBD tetramer (focused refinement)
Components
  • Glutamate receptor 1
  • Glutamate receptor 4
KeywordsSIGNALING PROTEIN / AMPA ionotropic glutamate receptor
Function / homology
Function and homology information


COPII-mediated vesicle transport / Cargo concentration in the ER / Activation of AMPA receptors / Trafficking of AMPA receptors / Trafficking of GluR2-containing AMPA receptors / Unblocking of NMDA receptors, glutamate binding and activation / axonal spine / cellular response to ammonium ion / dendritic spine membrane / long-term synaptic depression ...COPII-mediated vesicle transport / Cargo concentration in the ER / Activation of AMPA receptors / Trafficking of AMPA receptors / Trafficking of GluR2-containing AMPA receptors / Unblocking of NMDA receptors, glutamate binding and activation / axonal spine / cellular response to ammonium ion / dendritic spine membrane / long-term synaptic depression / perisynaptic space / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / AMPA glutamate receptor complex / excitatory synapse / long-term memory / synapse assembly / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / recycling endosome / postsynaptic density membrane / modulation of chemical synaptic transmission / receptor internalization / synaptic vesicle membrane / dendritic spine / neuronal cell body / glutamatergic synapse / cell surface / endoplasmic reticulum / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Chem-E2Q / Glutamate receptor / Glutamate receptor
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsSengupta, N. / Scrutton, A. / Greger, I.H. / Krieger, J.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105174197 United Kingdom
Wellcome Trust223194/Z/21/Z United Kingdom
CitationJournal: Science / Year: 2025
Title: Structure and organization of AMPA receptor-TARP complexes in the mammalian cerebellum.
Authors: Alexander M Scrutton / Nayanika Sengupta / Josip Ivica / Imogen Stockwell / Sew Peak-Chew / Bishal Singh / Kunimichi Suzuki / Veronica T Chang / Stephen H McLaughlin / James M Krieger / A ...Authors: Alexander M Scrutton / Nayanika Sengupta / Josip Ivica / Imogen Stockwell / Sew Peak-Chew / Bishal Singh / Kunimichi Suzuki / Veronica T Chang / Stephen H McLaughlin / James M Krieger / A Radu Aricescu / Ingo H Greger /
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 ...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.
History
DepositionJul 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor 1
B: Glutamate receptor 4
C: Glutamate receptor 1
D: Glutamate receptor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)394,8588
Polymers393,5134
Non-polymers1,3454
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Glutamate receptor 1


Mass: 99762.766 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Uniprot A0A286ZS63 (GRIA1 PIG), start 19 after signal peptide cleavage.
Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZS63
#2: Protein Glutamate receptor 4


Mass: 96993.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Uniprot I3L8N9 (GRIA4 PIG), start 22 after signal peptide cleavage.
Source: (natural) Sus scrofa (pig) / References: UniProt: I3L8N9
#3: Chemical
ChemComp-E2Q / 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide


Mass: 336.280 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H8N4O6S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cerebellar GluA1/4 LBD tetramer (focused refinement) / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
2RELION5particle selection
8UCSF ChimeraXmodel fitting
13cryoSPARC3D reconstruction
14PHENIXmodel refinement
15Cootmodel refinement
16REFMACmodel refinement
17ISOLDEmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 329869 / Symmetry type: POINT
Atomic model building

3D fitting-ID: 1

IDPDB-IDPdb chain-IDAccession codeChain-IDInitial refinement model-IDSource nameType
17OCE

7oce

A7OCEA1PDBexperimental model
2AF-I3L8N9-F12AlphaFoldin silico model
RefinementHighest resolution: 3.55 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028523
ELECTRON MICROSCOPYf_angle_d0.5711553
ELECTRON MICROSCOPYf_dihedral_angle_d9.9741214
ELECTRON MICROSCOPYf_chiral_restr0.0421292
ELECTRON MICROSCOPYf_plane_restr0.0041442

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