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

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Basic information

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
CitationJournal: 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-
UpdateSep 24, 2025-
Current statusSep 24, 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
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54246_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54246_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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