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


This is version 1.1 of the entry. See complete history


Literature

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

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

(2025) Nature 

  • DOI: https://doi.org/10.1038/s41586-025-09289-0
  • Primary Citation of 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.


Macromolecules
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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: 2Go to GlyGen: P19490-1
Sequence Annotations
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  • Reference Sequence
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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
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
11B8 scFv
E, F
257Mus musculusMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D 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 Glycosylation3D 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