Complex GGGN of AMPA-subtype iGluR GluA2 in complex with auxiliary subunit gamma2 (Stargazin) at low glutamate concentration (20 uM) in the presence of cyclothiazide (100 uM)

Experimental Data Snapshot

  • Resolution: 4.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Opening of glutamate receptor channel to subconductance levels.

Yelshanskaya, M.V.Patel, D.S.Kottke, C.M.Kurnikova, M.G.Sobolevsky, A.I.

(2022) Nature 605: 172-178

  • DOI: https://doi.org/10.1038/s41586-022-04637-w
  • Primary Citation of Related Structures:  
    7TNJ, 7TNK, 7TNL, 7TNM, 7TNN, 7TNO, 7TNP

  • PubMed Abstract: 

    Ionotropic glutamate receptors (iGluRs) are tetrameric ligand-gated ion channels that open their pores in response to binding of the agonist glutamate 1-3 . An ionic current through a single iGluR channel shows up to four discrete conductance levels (O1-O4) 4-6 . Higher conductance levels have been associated with an increased number of agonist molecules bound to four individual ligand-binding domains (LBDs) 6-10 . Here we determine structures of a synaptic complex of AMPA-subtype iGluR and the auxiliary subunit γ2 in non-desensitizing conditions with various occupancy of the LBDs by glutamate. We show that glutamate binds to LBDs of subunits B and D only after it is already bound to at least the same number of LBDs that belong to subunits A and C. Our structures combined with single-channel recordings, molecular dynamics simulations and machine-learning analysis suggest that channel opening requires agonist binding to at least two LBDs. Conversely, agonist binding to all four LBDs does not guarantee maximal channel conductance and favours subconductance states O1 and O2, with O3 and O4 being rare and not captured structurally. The lack of subunit independence and low efficiency coupling of glutamate binding to channel opening underlie the gating of synaptic complexes to submaximal conductance levels, which provide a potential for upregulation of synaptic activity.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform Flip of Glutamate receptor 2,Voltage-dependent calcium channel gamma-3 subunit chimera
A, B, C, D
1,033Rattus norvegicusMutation(s): 0 
Gene Names: Gria2Glur2
Membrane Entity: Yes 
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Find proteins for Q71RJ2 (Rattus norvegicus)
Explore Q71RJ2 
Go to UniProtKB:  Q71RJ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ71RJ2P19491
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 4.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS083660
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS107253
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA206573
National Science Foundation (NSF, United States)United States1818086

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 1.1: 2022-05-04
    Changes: Database references
  • Version 1.2: 2022-05-18
    Changes: Database references