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- EMDB-54543: Cerebellar GluA2/4 NTD heterophilic tetramer interface (focused r... -

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Basic information

Entry
Database: EMDB / ID: EMD-54543
TitleCerebellar GluA2/4 NTD heterophilic tetramer interface (focused refinement)
Map data
Sample
  • Complex: GluA2/4 NTD heterophilic tetramer interface (focused refinement)
    • Protein or peptide: Glutamate receptor 4
    • Protein or peptide: Glutamate receptor 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAMPA ionotropic glutamate receptor / SIGNALING PROTEIN
Function / homology
Function and homology information


Activation of AMPA receptors / Trafficking of AMPA receptors / Trafficking of GluR2-containing AMPA receptors / Unblocking of NMDA receptors, glutamate binding and activation / transmitter-gated monoatomic ion channel activity / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / AMPA glutamate receptor complex / 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 ...Activation of AMPA receptors / Trafficking of AMPA receptors / Trafficking of GluR2-containing AMPA receptors / Unblocking of NMDA receptors, glutamate binding and activation / transmitter-gated monoatomic ion channel activity / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / AMPA glutamate receptor complex / 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 / postsynaptic density membrane / modulation of chemical synaptic transmission / dendritic spine / postsynaptic membrane / cell surface receptor signaling pathway / glutamatergic synapse / 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
Glutamate receptor / Glutamate receptor
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsSengupta N / Scrutton A / Greger IH / Krieger JM
Funding support United Kingdom, 2 items
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 24, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54543.png

Downloads & links

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Map

FileDownload / File: emd_54543.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 360 pix.
= 343.8 Å		0.96 Å/pix.
x 360 pix.
= 343.8 Å		0.96 Å/pix.
x 360 pix.
= 343.8 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.955 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.3669631 - 2.2800028
Average (Standard dev.)0.005225036 (±0.061770782)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 343.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54543_msk_1.map
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Half map: #2

Fileemd_54543_half_map_1.map
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Half map: #1

Fileemd_54543_half_map_2.map
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Sample components

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Entire : GluA2/4 NTD heterophilic tetramer interface (focused refinement)

EntireName: GluA2/4 NTD heterophilic tetramer interface (focused refinement)
Components
  • Complex: GluA2/4 NTD heterophilic tetramer interface (focused refinement)
    • Protein or peptide: Glutamate receptor 4
    • Protein or peptide: Glutamate receptor 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: GluA2/4 NTD heterophilic tetramer interface (focused refinement)

SupramoleculeName: GluA2/4 NTD heterophilic tetramer interface (focused refinement)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: Glutamate receptor 4

MacromoleculeName: Glutamate receptor 4 / type: protein_or_peptide / ID: 1
Details: Uniprot I3L8N9 (GRIA4 PIG), start 22 after signal peptide cleavage.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 96.99375 KDa
SequenceString: AFPSSVQIGG LFIRNTDQEY TAFRLAIFLH NTSPNASEAP FNLVPHVDNI ETANSFAVTN AFCSQYSRGV FAIFGLYDKR SVHTLTSFC SALHISLITP SFPTEGESQF VLQLRPSLRG ALLSLLDHYE WNCFVFLYDT DRGYSILQAI MEKAGQNGWH V SAICVENF ...String:
AFPSSVQIGG LFIRNTDQEY TAFRLAIFLH NTSPNASEAP FNLVPHVDNI ETANSFAVTN AFCSQYSRGV FAIFGLYDKR SVHTLTSFC SALHISLITP SFPTEGESQF VLQLRPSLRG ALLSLLDHYE WNCFVFLYDT DRGYSILQAI MEKAGQNGWH V SAICVENF NDVSYRQLLE ELDRRQEKKF VIDCEIERLQ NILEQIVSVG KHVKGYHYII ANLGFKDISL ERFIHGGANV TG FQLVDFN TPMVTKLMDR WKKLDQREYP GSETPPKYTS ALTYDGVLVM AETFRNLRRQ KIDISRRGNA GDCLANPAAP WGQ GIDMER TLKQVQIQGL TGNVQFDHYG RRVNYTMDVF ELKSTGPRKV GYWNDMDKLV LIQDVPTLGN DTAAIENRTV VVTT IMESP YVMYKKNHEM FEGNDKYEGY CVDLASEIAK HIGIKYKIAI VPDGKYGARD ADTKIWNGMV GELVYGKAEI AIAPL TITL VREEVIDFSK PFMSLGISIM IKKPQKSKPG VFSFLDPLAY EIWMCIVFAY IGVSVVLFLV SRFSPYEWHT EEPEDG KEG PSDQPPNEFG IFNSLWFSLG AFMQQGCDIS PRSLSGRIVG GVWWFFTLII ISSYTANLAA FLTVERMVSP IESAEDL AK QTEIAYGTLD SGSTKEFFRR SKIAVYEKMW TYMRSAEPSV FTRTTAEGVA RVRKSKGKFA FLLESTMNEY IEQRKPCD T MKVGGNLDSK GYGVATPKGS SLRTPVNLAV LKLSEAGVLD KLKNKWWYDK GECGPKDSGS KDKTSALSLS NVAGVFYIL VGGLGLAMLV ALIEFCYKSR AEAKRMKVAK SAQTFNPTSS QNTQNLATYR EGYNVYGTES IKI

UniProtKB: Glutamate receptor

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Macromolecule #2: Glutamate receptor 2

MacromoleculeName: Glutamate receptor 2 / type: protein_or_peptide / ID: 2
Details: Uniprot A0A5G2QRQ2 (GRIA2 PIG), start 25 after signal peptide cleavage.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 92.309086 KDa
SequenceString: NSIQIGGLFP RGADQEYSAF RVGMVQFSTS EFRLTPHIDN LEVANSFAVT NAFCSQFSRG VYAIFGFYDK KSVNTITSFC GTLHVSFIT PSFPTDGTHP FVIQMRPDLK GALLSLIEYY QWDKFAYLYD SDRGLSTLQA VLDSAAEKKW QVTAINVGNI N NDKKDETY ...String:
NSIQIGGLFP RGADQEYSAF RVGMVQFSTS EFRLTPHIDN LEVANSFAVT NAFCSQFSRG VYAIFGFYDK KSVNTITSFC GTLHVSFIT PSFPTDGTHP FVIQMRPDLK GALLSLIEYY QWDKFAYLYD SDRGLSTLQA VLDSAAEKKW QVTAINVGNI N NDKKDETY RSLFQDLELK KERRVILDCE RDKVNDIVDQ VITIGKHVKG YHYIIANLGF TDGDLLKIQF GGANVSGFQI VD YDDSLVS KFIERWSTLE EKEYPGAHTT TIKYTSALTY DAVQVMTEAF RNLRKQRIEI SRRGNAGDCL ANPAVPWGQG VEI ERALKQ VQVEGLSGNI KFDQNGKRIN YTINIMELKT NGPRKIGYWS EVDKMVVTLT ELPSGNDTSG LENKTVVVTT ILES PYVMM KKNHEMLEGN ERYEGYCVDL AAEIAKHCGF KYKLTIVGDG KYGARDADTK IWNGMVGELV YGKADIAIAP LTITL VREE VIDFSKPFMS LGISIMIKKP QKSKPGVFSF LDPLAYEIWM CIVFAYIGVS VVLFLVSRFS PYEWHTEEFE DGRETQ SSE STNEFGIFNS LWFSLGAFMQ QGCDISPRSL SGRIVGGVWW FFTLIIISSY TANLAAFLTV ERMVSPIESA EDLSKQT EI AYGTLDSGST KEFFRRSKIA VFDKMWTYMR SAEPSVFVRT TAEGVARVRK SKGKYAYLLE STMNEYIEQR KPCDTMKV G GNLDSKGYGI ATPKGSSLRW EKTSALSLSN VAGVFYILVG GLGLAMLVAL IEFCYKSRAE AKRMKVAKNA QNINPSSSQ NSQNFATYKE GYNVYGIESV KI

UniProtKB: Glutamate receptor

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 30603
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

9b68

source_name: PDB, initial_model_type: experimental model

9-f1

source_name: AlphaFold, initial_model_type: in silico model
Output model

PDB-9s3o:
Cerebellar GluA2/4 NTD heterophilic tetramer interface (focused refinement)

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