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- EMDB-55413: GluA4 N-terminal domain bound to nanobody NB74 (focused refinement) -

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Basic information

Entry
Database: EMDB / ID: EMD-55413
TitleGluA4 N-terminal domain bound to nanobody NB74 (focused refinement)
Map data
Sample
  • Complex: GluA4 N-terminal domain bound to nanobody NB74 (focused refinement)
KeywordsAMPA ionotropic glutamate receptor / SIGNALING PROTEIN
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 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
DepositionOct 20, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55413.png

Downloads & links

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Map

FileDownload / File: emd_55413.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.)
0.96 Å/pix.
x 512 pix.
= 488.96 Å		0.96 Å/pix.
x 512 pix.
= 488.96 Å		0.96 Å/pix.
x 512 pix.
= 488.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.955 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.288
Minimum - Maximum-0.579914 - 1.2708912
Average (Standard dev.)-0.00008360879 (±0.032031428)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 488.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_55413_half_map_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_55413_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 : GluA4 N-terminal domain bound to nanobody NB74 (focused refinement)

EntireName: GluA4 N-terminal domain bound to nanobody NB74 (focused refinement)
Components
  • Complex: GluA4 N-terminal domain bound to nanobody NB74 (focused refinement)

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Supramolecule #1: GluA4 N-terminal domain bound to nanobody NB74 (focused refinement)

SupramoleculeName: GluA4 N-terminal domain bound to nanobody NB74 (focused refinement)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Rattus norvegicus (Norway rat)

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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: TFS Selectris X
Image recordingFilm or detector model: FEI FALCON IV (4k 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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 46065
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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