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- EMDB-66939: The LBD-TMD structure of homomeric GluA4 AMPA receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-66939
TitleThe LBD-TMD structure of homomeric GluA4 AMPA receptor
Map data
Sample
  • Complex: The LBD-TMD structure of homomeric GluA4 AMPA receptor
    • Protein or peptide: Glutamate receptor 4
KeywordsAMPA receptor / native / GluA1 / GluA4 / LBD / TMD / CNIH3 / active state / MEMBRANE PROTEIN
Function / homology
Function and homology information


Activation of AMPA receptors / Synaptic adhesion-like molecules / Unblocking of NMDA receptors, glutamate binding and activation / Trafficking of GluR2-containing AMPA receptors / Trafficking of AMPA receptors / kainate selective glutamate receptor complex / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / AMPA glutamate receptor complex / glutamate-gated receptor activity ...Activation of AMPA receptors / Synaptic adhesion-like molecules / Unblocking of NMDA receptors, glutamate binding and activation / Trafficking of GluR2-containing AMPA receptors / Trafficking of AMPA receptors / kainate selective glutamate receptor complex / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / AMPA glutamate receptor complex / glutamate-gated receptor activity / positive regulation of synaptic transmission, glutamatergic / presynaptic active zone membrane / 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 / terminal bouton / dendritic spine / chemical synaptic transmission / postsynaptic density / neuronal cell body / synapse / dendrite / glutamatergic synapse / identical protein binding / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / 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 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLi X / Li R / Wei Y / Zhao Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92157102 China
CitationJournal: Cell Res / Year: 2026
Title: Assembly and gating mechanism of native AMPA receptors from the cerebellum.
Authors: Xiaojing Li / Renjie Li / Yiqing Wei / Jiexin Chen / Jiaojiao Zhao / Jun Zhao / Wei Wang / Na Li / Lili Wang / Tuo Hu / Yanli Dong / Yongping Zhu / Chao Wei / Long Li / Wei Zhang / Zhuo Huang / Yan Zhao /
Abstract: AMPA receptors (AMPARs) mediate the majority of fast excitatory synaptic transmission throughout the central nervous system. Calcium-permeable AMPARs and GluA4-containing receptors are critical for ...AMPA receptors (AMPARs) mediate the majority of fast excitatory synaptic transmission throughout the central nervous system. Calcium-permeable AMPARs and GluA4-containing receptors are critical for cerebellar functions, such as motor learning, associative memory, auditory processing, and synaptic plasticity. In contrast to the well-characterized, predominantly GluA2-containing AMPARs of the hippocampus and cortex, cerebellar AMPARs contain a higher proportion of GluA4 and remain poorly understood. Here, we generated a highly GluA4-specific antibody. Using this antibody in combination with antibodies specifically recognizing GluA1 and GluA2, we purified native AMPARs and determined the subunit compositions of both calcium-impermeable and calcium-permeable native AMPARs in the cerebellum. The isolated cerebellar AMPARs that contained both GluA1 and GluA4 were calcium-permeable, with GluA4 occupying mainly the B/D positions, GluA1 occupying the A/C positions, and the complex associated primarily with cornichon 3 (CNIH3). We determined the structures of the complex in distinct functional states, including the resting, active, and desensitized states, and characterized the conformational transitions that underlie its activity. During desensitization, the receptor adopts a pseudo-4-fold configuration of the ligand-binding domain layer, which may be important for its functional properties. This study provides a blueprint for the subunit compositions of AMPARs in the cerebellum and clarifies the gating mechanism of the calcium-permeable native AMPAR-CNIH3 complex, providing significant insight into AMPAR-mediated synaptic transmission in the cerebellum.
History
DepositionNov 4, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66939.png

Downloads & links

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Map

FileDownload / File: emd_66939.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 400 pix.
= 340. Å		0.85 Å/pix.
x 400 pix.
= 340. Å		0.85 Å/pix.
x 400 pix.
= 340. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.37590778 - 0.6329203
Average (Standard dev.)0.00066513143 (±0.014982977)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 340.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_66939_half_map_1.map
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Half map: #2

Fileemd_66939_half_map_2.map
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Sample components

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Entire : The LBD-TMD structure of homomeric GluA4 AMPA receptor

EntireName: The LBD-TMD structure of homomeric GluA4 AMPA receptor
Components
  • Complex: The LBD-TMD structure of homomeric GluA4 AMPA receptor
    • Protein or peptide: Glutamate receptor 4

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Supramolecule #1: The LBD-TMD structure of homomeric GluA4 AMPA receptor

SupramoleculeName: The LBD-TMD structure of homomeric GluA4 AMPA receptor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Glutamate receptor 4

MacromoleculeName: Glutamate receptor 4 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 47.801094 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RTVVVTTIME SPYVMYKKNH EMFEGNDKYE GYCVDLASEI AKHIGIKYKI AIVPDGKYGA RDADTKIWNG MVGELVYGKA EIAIAPLTI TLVREEVIDF SKPFMSLGIS IMIKKPQKSK PGVFSFLDPL AYEIWMCIVF AYIGVSVVLF LVSRFSPYEW H TEEPEDGK ...String:
RTVVVTTIME SPYVMYKKNH EMFEGNDKYE GYCVDLASEI AKHIGIKYKI AIVPDGKYGA RDADTKIWNG MVGELVYGKA EIAIAPLTI TLVREEVIDF SKPFMSLGIS IMIKKPQKSK PGVFSFLDPL AYEIWMCIVF AYIGVSVVLF LVSRFSPYEW H TEEPEDGK EGPSDQPPNE FGIFNSLWFS LGAFMQQGCD ISPRSLSGRI VGGVWWFFTL IIISSYTANL AAFLTVERMV SP IESAEDL AKQTEIAYGT LDSGSTKEFF RRSKIAVYEK MWTYMRSAEP SVFTRTTAEG VARVRKSKGK FAFLLESTMN EYI EQRKPC DTMKVGGNLD SKGYGVATPK GSSLRTPVNL AVLKLSEAGV LDKLKNKWWY DKGECGPKDS GSKDKTSALS LSNV AGVFY ILVGGLGLAM LVALIEFCYK SRAE

UniProtKB: Glutamate receptor 4

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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
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 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 ONLY
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 21592
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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