9HPE | pdb_00009hpe

The NTD dimer and the interfacing LBD region of the AMPAR complex GluA3- TARP gamma2 in the apo state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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

Architecture, dynamics and biogenesis of GluA3 AMPA glutamate receptors.

Pokharna, A.Stockwell, I.Ivica, J.Singh, B.Schwab, J.Vega-Gutierrez, C.Herguedas, B.Cais, O.Krieger, J.M.Greger, I.H.

(2025) Nature 

  • DOI: https://doi.org/10.1038/s41586-025-09325-z
  • Primary Citation of Related Structures:  
    9HPC, 9HPD, 9HPE, 9HPF, 9HPG, 9HPK, 9QFH

  • PubMed Abstract: 

    AMPA-type glutamate receptors (AMPARs) mediate the majority of excitatory neurotransmission in the brain 1 . Assembled from combinations of four core subunits, GluA1-4, and ~20 auxiliary subunits, their molecular diversity tunes information transfer and storage in a brain circuit-specific manner. GluA3, a subtype strongly associated with disease 2 , functions as both a fast transmitting Ca 2+ -permeable (CP) AMPAR at sensory synapses 3 , and as a Ca 2+ -impermeable (CI) receptor at cortical synapses 4,5 . Here, we present cryo-EM structures of the CP GluA3 homomer, which substantially diverge from other AMPARs. The GluA3 extracellular domain tiers (NTD and LBD) are closely coupled throughout gating states, creating previously unseen interfaces that impact signalling and harbour human disease mutations. Central to this architecture is a stacking interaction between two arginine residues (Arg163) in the NTD dimer interface, trapping a unique NTD dimer conformation that enables close contacts with the LBD. Rupture of the Arg163 stack not only alters the structure and dynamics of the GluA3 extracellular region, but also increases receptor trafficking, and the expression of GluA3 heteromers at the synapse. We further show that a mammalian-specific GluA3 trafficking checkpoint determines conformational stability of the LBD tier. Hence, specific design features define communication and biogenesis of GluA3, offering a framework to interrogate this disease-prone glutamate receptor.


  • Organizational Affiliation

    Neurobiology Division, Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunitA [auth B],
B [auth C]
1,179Rattus norvegicusMutation(s): 1 
Gene Names: Gria3GluA3Glur3Cacng2Stg
UniProt
Find proteins for P19492 (Rattus norvegicus)
Explore P19492 
Go to UniProtKB:  P19492
Find proteins for Q71RJ2 (Rattus norvegicus)
Explore Q71RJ2 
Go to UniProtKB:  Q71RJ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ71RJ2P19492
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q71RJ2-1P19492-1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom223194/Z/21/Z
Medical Research Council (MRC, United Kingdom)United KingdomMC_U105174197

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection, Database references, Structure summary