9B61

GluA2 flip Q in complex with TARPgamma2 at pH5, consensus structure of LBD-TMD-TARPgamma2

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Mus musculus, Rattus norvegicus
  • Expression System: Homo sapiens
  • Mutation(s): No 
  • Membrane Protein: Yes  PDBTM

  • Deposited: 2024-03-23 Released: 2024-07-31 
  • Deposition Author(s): Nakagawa, T., Greger, I.H.
  • Funding Organization(s): National Institutes of Health/National Institute of Mental Health (NIH/NIMH), UK Research and Innovation (UKRI), Biotechnology and Biological Sciences Research Council (BBSRC), Wellcome Trust

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Proton-triggered rearrangement of the AMPA receptor N-terminal domains impacts receptor kinetics and synaptic localization.

Ivica, J.Kejzar, N.Ho, H.Stockwell, I.Kuchtiak, V.Scrutton, A.M.Nakagawa, T.Greger, I.H.

(2024) Nat Struct Mol Biol 31: 1601-1613

  • DOI: https://doi.org/10.1038/s41594-024-01369-5
  • Primary Citation of Related Structures:  
    9B5Z, 9B60, 9B61, 9B63, 9B64, 9B67, 9B68, 9B69, 9B6A

  • PubMed Abstract: 

    AMPA glutamate receptors (AMPARs) are ion channel tetramers that mediate the majority of fast excitatory synaptic transmission. They are composed of four subunits (GluA1-GluA4); the GluA2 subunit dominates AMPAR function throughout the forebrain. Its extracellular N-terminal domain (NTD) determines receptor localization at the synapse, ensuring reliable synaptic transmission and plasticity. This synaptic anchoring function requires a compact NTD tier, stabilized by a GluA2-specific NTD interface. Here we show that low pH conditions, which accompany synaptic activity, rupture this interface. All-atom molecular dynamics simulations reveal that protonation of an interfacial histidine residue (H208) centrally contributes to NTD rearrangement. Moreover, in stark contrast to their canonical compact arrangement at neutral pH, GluA2 cryo-electron microscopy structures exhibit a wide spectrum of NTD conformations under acidic conditions. We show that the consequences of this pH-dependent conformational control are twofold: rupture of the NTD tier slows recovery from desensitized states and increases receptor mobility at mouse hippocampal synapses. Therefore, a proton-triggered NTD switch will shape both AMPAR location and kinetics, thereby impacting synaptic signal transmission.


  • 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
Voltage-dependent calcium channel gamma-2 subunitA [auth H],
B [auth F],
G [auth E],
H [auth G]
323Mus musculusMutation(s): 0 
Gene Names: Cacng2Stg
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O88602 (Mus musculus)
Explore O88602 
Go to UniProtKB:  O88602
IMPC:  MGI:1316660
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO88602
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform Flip of Glutamate receptor 2C,
D [auth B],
E [auth A],
F [auth D]
889Rattus norvegicusMutation(s): 0 
Gene Names: Gria2Glur2
Membrane Entity: Yes 
UniProt
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19491
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:
RECONSTRUCTIONRELION4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesR01MH123474
UK Research and Innovation (UKRI)United KingdomMC_U105174197
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/N002113/1
Wellcome TrustUnited Kingdom223194/Z/21/Z

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 1.1: 2024-08-21
    Changes: Data collection, Database references
  • Version 1.2: 2024-09-04
    Changes: Data collection, Database references
  • Version 1.3: 2024-10-16
    Changes: Data collection, Structure summary
  • Version 1.4: 2024-10-30
    Changes: Data collection, Database references