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- EMDB-61335: native AMPA receptors from cerebellum -

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Basic information

Entry
Database: EMDB / ID: EMD-61335
Titlenative AMPA receptors from cerebellum
Map data
Sample
  • Complex: native AMPA receptors from cerebellum
KeywordsAMPA receptor / native / GluA4 / GluA1 / MEMBRANE PROTEIN
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.81 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
DepositionAug 27, 2024-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61335.png

Downloads & links

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Map

FileDownload / File: emd_61335.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 450 pix.
= 495. Å		1.1 Å/pix.
x 450 pix.
= 495. Å		1.1 Å/pix.
x 450 pix.
= 495. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.5904015 - 1.1130016
Average (Standard dev.)-0.000794794 (±0.024863785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 495.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61335_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_61335_half_map_2.map
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Sample components

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Entire : native AMPA receptors from cerebellum

EntireName: native AMPA receptors from cerebellum
Components
  • Complex: native AMPA receptors from cerebellum

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Supramolecule #1: native AMPA receptors from cerebellum

SupramoleculeName: native AMPA receptors from cerebellum / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Sus scrofa (pig)

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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 / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN 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: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26240
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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