9NRA | pdb_00009nra

The structure of GluA1/A4 LBD-TMD with 4 auxiliary subunits


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Gating and noelin clustering of native Ca 2+ -permeable AMPA receptors.

Fang, C.L.Spangler, C.J.Park, J.Sheldon, N.Trussell, L.O.Gouaux, E.

(2025) Nature 645: 526-534

  • DOI: https://doi.org/10.1038/s41586-025-09289-0
  • Primary Citation Related Structures: 
    9NR6, 9NR7, 9NR8, 9NR9, 9NRA

  • PubMed Abstract: 

    AMPA-type ionotropic glutamate receptors (AMPARs) are integral to fast excitatory synaptic transmission and play vital roles in synaptic plasticity, motor coordination, learning, and memory 1 . While extensive structural studies have been conducted on recombinant AMPARs and native calcium impermeable (CI)-AMPARs alongside their auxiliary proteins 2-5 , the molecular architecture of native calcium permeable (CP)-AMPARs has remained undefined. To elucidate the subunit composition, physiological architecture, and gating mechanisms of CP-AMPARs, here we present the first visualization of these receptors, immunoaffinity purified from rat cerebella, and resolve their structures using cryo-electron microscopy (cryo-EM). Our results indicate that the predominant assembly consists of GluA1 and GluA4 subunits, with the GluA4 subunit occupying the B and D positions, while auxiliary subunits, including TARPs, are located at the B'/D' positions and CNIHs or TARPs at the A'/C' positions. Furthermore, we resolved the structure of the Noelin 1-GluA1/A4 complex, wherein Noelin 1 (Noe 1) specifically binds to the GluA4 subunit at the B and D positions. Notably, Noe 1 stabilizes the amino-terminal domain (ATD) layer without affecting receptor gating properties. Noe 1 contributes to AMPAR function by forming dimeric-AMPAR assemblies that likely engage in extracellular networks, clustering receptors within synaptic environments and modulating receptor responsiveness to synaptic inputs.


  • Organizational Affiliation
    • Vollum Institute, Oregon Health & Science University, Portland, OR, USA.

Macromolecule Content 

  • Total Structure Weight: 256.9 kDa 
  • Atom Count: 15,598 
  • Modeled Residue Count: 2,195 
  • Deposited Residue Count: 2,344 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor 1
A, C
427Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P19490 (Rattus norvegicus)
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UniProt GroupP19490
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 2 of Glutamate receptor 4
B, D
424Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P19493 (Rattus norvegicus)
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UniProt GroupP19493
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Auxiliary protein at A'/C'
E, G
117Rattus norvegicusMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Voltage-dependent calcium channel gamma-2 subunit
F, H
204Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q71RJ2 (Rattus norvegicus)
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UniProt GroupQ71RJ2
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2025-07-09
    Changes: Data collection, Database references
  • Version 1.2: 2025-09-17
    Changes: Data collection, Database references
  • Version 1.3: 2025-11-26
    Changes: Data collection, Database references, Structure summary