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- EMDB-54556: Cerebellar GluA1/4 LBD tetramer (focused refinement) -

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Basic information

Entry
Database: EMDB / ID: EMD-54556
TitleCerebellar GluA1/4 LBD tetramer (focused refinement)
Map data
Sample
  • Complex: Cerebellar GluA1/4 LBD tetramer (focused refinement)
    • Protein or peptide: Glutamate receptor 1
    • Protein or peptide: Glutamate receptor 4
  • Ligand: 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide
KeywordsAMPA ionotropic glutamate receptor / SIGNALING PROTEIN
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
Glutamate receptor / Glutamate receptor
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 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 25, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54556.png

Downloads & links

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Map

FileDownload / File: emd_54556.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 440 pix.
= 363.44 Å		0.83 Å/pix.
x 440 pix.
= 363.44 Å		0.83 Å/pix.
x 440 pix.
= 363.44 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.48
Minimum - Maximum-2.3208585 - 3.710358
Average (Standard dev.)0.0011038112 (±0.044965044)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 363.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54556_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54556_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Cerebellar GluA1/4 LBD tetramer (focused refinement)

EntireName: Cerebellar GluA1/4 LBD tetramer (focused refinement)
Components
  • Complex: Cerebellar GluA1/4 LBD tetramer (focused refinement)
    • Protein or peptide: Glutamate receptor 1
    • Protein or peptide: Glutamate receptor 4
  • Ligand: 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide

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Supramolecule #1: Cerebellar GluA1/4 LBD tetramer (focused refinement)

SupramoleculeName: Cerebellar GluA1/4 LBD tetramer (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 1

MacromoleculeName: Glutamate receptor 1 / type: protein_or_peptide / ID: 1
Details: Uniprot A0A286ZS63 (GRIA1 PIG), start 19 after signal peptide cleavage.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 99.762766 KDa
SequenceString: ANFPNNIQIG GLFPNQQSQE HAAFRFALSQ LTEPPKLLPQ IDIVNISDSF EMTYRFCSQF SKGVYAIFGF YERRTVNMLT SFCGALHVC FITPSFPVDT SNQFVLQLRP ELQDALISII DHYKWQKFVY IYDADRGLSV LQKVLDTAAE KNWQVTAVNI L TTTEEGYR ...String:
ANFPNNIQIG GLFPNQQSQE HAAFRFALSQ LTEPPKLLPQ IDIVNISDSF EMTYRFCSQF SKGVYAIFGF YERRTVNMLT SFCGALHVC FITPSFPVDT SNQFVLQLRP ELQDALISII DHYKWQKFVY IYDADRGLSV LQKVLDTAAE KNWQVTAVNI L TTTEEGYR MLFQDLEKKK ERLVVVDCES ERLNAILGQI IKLEKNGIGY HYILANLGFM DIDLNKFKES GANVTGFQLV NY TDTIPAK IMQQWKTSDA RDHTRVDWKR PKYTSALTYD GVKVMAEAFQ SLRRQRIDIS RRGNAGDCLA NPAVPWGQGI DIQ RALQQV RFEGLTGNVQ FNEKGRRTNY TLHVIEMKHD GIRKIGYWNE DDKFVPAATD AQAGGDNSSV QNRTYIVTTI LEDP YVMLK KNANQFEGND RYEGYCVELA AEIAKHVGYS YRLEIVSDGK YGARDPDTKA WNGMVGELVY GRADVAVAPL TITLV REEV IDFSKPFMSL GISIMIKKPQ KSKPGVFSFL DPLAYEIWMC IVFAYIGVSV VLFLVSRFSP YEWHSEEFEE GRDQTT SDQ SNEFGIFNSL WFSLGAFMQQ GCDISPRSLS GRIVGGVWWF FTLIIISSYT ANLAAFLTVE RMVSPIESAE DLAKQTE IA YGTLEAGSTK EFFRRSKIAV FEKMWTYMKS AEPSVFVRTT EEGMIRVRKS KGKYAYLLES TMNEYIEQRK PCDTMKVG G NLDSKGYGIA TPKGSALRNP VNLAVLKLNE QGLLDKLKNK WWYDKGECGS KDSGSKDKTS ALSLSNVAGV FYILIGGLG LAMLVALIEF CYKSRSESKR MKGFCLIPQQ SINEAIRTST LPRNSGAGAS GGGSGENGRV VSHDFPKSMQ SIPCMSHSTG MPLGATGL

UniProtKB: Glutamate receptor

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Macromolecule #2: Glutamate receptor 4

MacromoleculeName: Glutamate receptor 4 / type: protein_or_peptide / ID: 2
Details: Uniprot I3L8N9 (GRIA4 PIG), start 22 after signal peptide cleavage.
Number of copies: 2 / 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 #3: 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-s...

MacromoleculeName: 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide
type: ligand / ID: 3 / Number of copies: 4 / Formula: E2Q
Molecular weightTheoretical: 336.28 Da
Chemical component information

ChemComp-E2Q:
6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide

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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: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 329869
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

7oce

chain_id: A, source_name: PDB, initial_model_type: experimental model

9-f1

source_name: AlphaFold, initial_model_type: in silico model
Output model

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

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