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- EMDB-54246: Subtomogram average of an ionotropic glutamate receptor within ma... -

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Entry
Database: EMDB / ID: EMD-54246
TitleSubtomogram average of an ionotropic glutamate receptor within mammalian glutamatergic synapses
Map dataSubtomogram average of an ionotropic glutamate receptor from mammalian synapses
Sample
  • Complex: Inotropic glutamate receptor (iGluR)
Keywordsglutamate receptor / Synapse / Neurotransmission / Ion channel / SIGNALING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 25.0 Å
AuthorsPeukes J / Frank R / Briggs JAG
Funding supportEuropean Union, United Kingdom, 7 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-CoG-648432 MEMBRANEFUSIONEuropean Union
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
UK Research and Innovation (UKRI)MR/V022644/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011151/1 United Kingdom
European Research Council (ERC)695568 SYNNOVATEEuropean Union
Medical Research Council (MRC, United Kingdom)MC_UP_1201/8 United Kingdom
Wellcome TrustSBF005/1046 United Kingdom
Citation
Journal: Elife / Year: 2025
Title: The molecular infrastructure of glutamatergic synapses in the mammalian forebrain.
Authors: Julia Peukes / Charlie Lovatt / Conny Leistner / Jerome Boulanger / Dustin R Morado / Martin J G Fuller / Wanda Kukulski / Fei Zhu / Noboru H Komiyama / John A G Briggs / Seth G N Grant / René A W Frank /
Abstract: Glutamatergic synapses form the vast majority of connections within neuronal circuits, but how these subcellular structures are molecularly organized within the mammalian brain is poorly understood. ...Glutamatergic synapses form the vast majority of connections within neuronal circuits, but how these subcellular structures are molecularly organized within the mammalian brain is poorly understood. Conventional electron microscopy using chemically fixed, metal-stained tissue has identified a proteinaceous, membrane-associated thickening called the 'postsynaptic density' (PSD). Here, we combined mouse genetics and cryo-electron tomography to determine the 3D molecular architecture of fresh isolated and anatomically intact synapses in the adult forebrain. The native glutamatergic synapse did not consistently show a higher density of proteins at the postsynaptic membrane, thought to be characteristic of the PSD. Instead, a 'synaptoplasm' consisting of cytoskeletal elements, macromolecular complexes, and membrane-bound organelles extended throughout the pre- and post-synaptic compartments. Snapshots of active processes gave insights into membrane remodeling processes. Clusters of up to 60 ionotropic glutamate receptors were positioned inside and outside the synaptic cleft. Together, these information-rich tomographic maps present a detailed molecular framework for the coordinated activity of synapses in the adult mammalian brain.
#1: Journal: eLife / Year: 2024
Title: The molecular infrastructure of glutamatergic synapses in the mammalian forebrain
Authors: Peukes J / Lovatt C / Leistner C / Boulanger J / Morado DR / Fuller MJG / Kukulski W / Zhu F / Komiyama NH / Briggs JAG / Grant SGN / Frank RAW
History
DepositionJul 2, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54246.png

Downloads & links

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Map

FileDownload / File: emd_54246.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of an ionotropic glutamate receptor from mammalian synapses
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
5.97 Å/pix.
x 96 pix.
= 573.12 Å		5.97 Å/pix.
x 96 pix.
= 573.12 Å		5.97 Å/pix.
x 96 pix.
= 573.12 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 5.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.76974773 - 0.85207
Average (Standard dev.)0.00067972636 (±0.06785162)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 573.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54246_msk_1.map
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Half map: #2

Fileemd_54246_half_map_1.map
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Half map: #1

Fileemd_54246_half_map_2.map
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Sample components

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Entire : Inotropic glutamate receptor (iGluR)

EntireName: Inotropic glutamate receptor (iGluR)
Components
  • Complex: Inotropic glutamate receptor (iGluR)

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Supramolecule #1: Inotropic glutamate receptor (iGluR)

SupramoleculeName: Inotropic glutamate receptor (iGluR) / type: complex / ID: 1 / Parent: 0 / Details: Predominantly AMPA subtype
Source (natural)Organism: Mus musculus (house mouse) / Strain: PSD95-GFP knockin mouse / Organ: Brain / Tissue: Brain / Location in cell: Postsynaptic membrane

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statetissue

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Sample preparation

BufferpH: 7.4
Details: 125 mM NaCl, 25 mM KCl, 25 mM NHCO3, 25 mM glucose, 2.5 mM KCl, 2 mM CaCl2, 1.25 mM NaH2PO4, 1 mM MgCl2; Osmolality: 310 mOsM/L
GridModel: Quantifoil / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 6e-05 kPa
VitrificationCryogen name: ETHANE / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsMouse forebrain homogeneized in artificial cerebrospinal fluid (ACSF) to generate suspension of Psd95-GFP containing synaptoneurosomes. Samples was applied to cryoEM grid and plunge frozen in liquid ethane. CryET dataset collection was guided by Psd95-GFP cryoCLEM.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.25 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 42000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 2368
ExtractionNumber tomograms: 93 / Number images used: 2522 / Method: Manual picking
CTF correctionType: NONE
Final angle assignmentType: NOT APPLICABLE

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