9NR8 | pdb_00009nr8

The structure of cerebellar GluA1/A4 ATD


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9NR8

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: 231.72 kDa 
  • Atom Count: 14,576 
  • Modeled Residue Count: 1,958 
  • Deposited Residue Count: 2,016 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor 1
A, C
373Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P19490 (Rattus norvegicus)
Explore P19490 
Go to UniProtKB:  P19490
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19490
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P19490-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor 4
B, D
378Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P19493 (Rattus norvegicus)
Explore P19493 
Go to UniProtKB:  P19493
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19493
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P19493-1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
11B8 scFv
E, F
257Mus musculusMutation(s): 0 

Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth I],
H [auth J]
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I [auth N],
J [auth G],
K [auth H],
L [auth K],
M [auth L],
I [auth N],
J [auth G],
K [auth H],
L [auth K],
M [auth L],
N [auth M]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 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