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- PDB-9j95: Native GluA1/GluA4-CNIH3 complex in desensitized state -

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Basic information

Entry
Database: PDB / ID: 9j95
TitleNative GluA1/GluA4-CNIH3 complex in desensitized state
Components
  • (Glutamate receptor) x 2
  • Cornichon family AMPA receptor auxiliary protein 3
KeywordsMEMBRANE PROTEIN / AMPA receptor / native / GluA1 / GluA4 / CNIH3 / desensitized state
Function / homology
Function and homology information


COPII-mediated vesicle transport / Cargo concentration in the ER / Activation of AMPA receptors / Trafficking of AMPA receptors / Trafficking of GluR2-containing AMPA receptors / Unblocking of NMDA receptors, glutamate binding and activation / axonal spine / cellular response to ammonium ion / dendritic spine membrane / long-term synaptic depression ...COPII-mediated vesicle transport / Cargo concentration in the ER / Activation of AMPA receptors / Trafficking of AMPA receptors / Trafficking of GluR2-containing AMPA receptors / Unblocking of NMDA receptors, glutamate binding and activation / axonal spine / cellular response to ammonium ion / dendritic spine membrane / long-term synaptic depression / perisynaptic space / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / AMPA glutamate receptor complex / long-term memory / vesicle-mediated transport / synapse assembly / excitatory synapse / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / receptor internalization / recycling endosome / postsynaptic density membrane / modulation of chemical synaptic transmission / synaptic vesicle membrane / dendritic spine / signaling receptor binding / neuronal cell body / synapse / dendrite / glutamatergic synapse / cell surface / endoplasmic reticulum / membrane / plasma membrane
Similarity search - Function
Cornichon / Cornichon, conserved site / Cornichon protein / Cornichon family signature. / Cornichon / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site ...Cornichon / Cornichon, conserved site / Cornichon protein / Cornichon family signature. / Cornichon / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / 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 / Cornichon family AMPA receptor auxiliary protein 3 / Glutamate receptor
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.26 Å
AuthorsLi, X. / Li, R. / Wei, Y. / Zhao, Y.
Funding support China, 1items
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 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor
B: Glutamate receptor
C: Glutamate receptor
D: Glutamate receptor
E: Cornichon family AMPA receptor auxiliary protein 3
F: Cornichon family AMPA receptor auxiliary protein 3
G: Cornichon family AMPA receptor auxiliary protein 3
H: Cornichon family AMPA receptor auxiliary protein 3


Theoretical massNumber of molelcules
Total (without water)477,3658
Polymers477,3658
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Glutamate receptor


Mass: 101565.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZS63
#2: Protein Glutamate receptor


Mass: 99389.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3L8N9
#3: Protein
Cornichon family AMPA receptor auxiliary protein 3


Mass: 18863.311 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BJP0
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Native GluA1/GluA4-CNIH3 complex in desensitized state
Type: COMPLEX / Entity ID: #1, #3, #2 / Source: NATURAL
Source (natural)Organism: Sus scrofa (pig)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 4.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20638 / Symmetry type: POINT

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