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- EMDB-66940: The ATD structure of homomeric GluA4 AMPA receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-66940
TitleThe ATD structure of homomeric GluA4 AMPA receptor
Map data
Sample
  • Complex: The ATD structure of homomeric GluA4 AMPA receptor
    • Protein or peptide: Glutamate receptor 4
KeywordsAMPA receptor / native / GluA1 / GluA4 / LBD / TMD / CNIH3 / active state / MEMBRANE PROTEIN / 1D8
Function / homology
Function and homology information


Activation of AMPA receptors / Synaptic adhesion-like molecules / Trafficking of GluR2-containing AMPA receptors / Unblocking of NMDA receptors, glutamate binding and activation / 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 / positive regulation of synaptic transmission, glutamatergic ...Activation of AMPA receptors / Synaptic adhesion-like molecules / Trafficking of GluR2-containing AMPA receptors / Unblocking of NMDA receptors, glutamate binding and activation / 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 / positive regulation of synaptic transmission, glutamatergic / glutamate-gated receptor activity / presynaptic active zone membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / dendritic spine / chemical synaptic transmission / postsynaptic density / neuronal cell body / dendrite / synapse / glutamatergic synapse / identical protein binding / 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 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 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: Li X / Li R / Wei Y / Chen J / Zhao J / Zhao J / Wang W / Li N / Wang L / Hu T / Dong Y / Zhu Y / Wei C / Li L / Zhang W / Huang Z / Zhao Y
History
DepositionNov 4, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66940.png

Downloads & links

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Map

FileDownload / File: emd_66940.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 512 pix.
= 435.2 Å		0.85 Å/pix.
x 512 pix.
= 435.2 Å		0.85 Å/pix.
x 512 pix.
= 435.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.23319383 - 0.6240692
Average (Standard dev.)-0.0003622982 (±0.017880412)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_66940_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66940_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The ATD structure of homomeric GluA4 AMPA receptor

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

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Supramolecule #1: The ATD structure of homomeric GluA4 AMPA receptor

SupramoleculeName: The ATD 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: 43.388133 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GAFPSSVQIG GLFIRNTDQE YTAFRLAIFL HNTSPNASEA PFNLVPHVDN IETANSFAVT NAFCSQYSRG VFAIFGLYDK RSVHTLTSF CSALHISLIT PSFPTEGESQ FVLQLRPSLR GALLSLLDHY EWNCFVFLYD TDRGYSILQA IMEKAGQNGW H VSAICVEN ...String:
GAFPSSVQIG GLFIRNTDQE YTAFRLAIFL HNTSPNASEA PFNLVPHVDN IETANSFAVT NAFCSQYSRG VFAIFGLYDK RSVHTLTSF CSALHISLIT PSFPTEGESQ FVLQLRPSLR GALLSLLDHY EWNCFVFLYD TDRGYSILQA IMEKAGQNGW H VSAICVEN FNDVSYRQLL EELDRRQEKK FVIDCEIERL QNILEQIVSV GKHVKGYHYI IANLGFKDIS LERFIHGGAN VT GFQLVDF NTPMVTKLMD RWKKLDQREY PGSETPPKYT SALTYDGVLV MAETFRSLRR QKIDISRRGN AGDCLANPAA PWG QGIDME RTLKQVRIQG LTGNVQFDHY GRRVNYTMDV FELKSTGPRK VGYWNDMDKL VLIQD

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: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 6398
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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