Crystal structure of the GluK2EM LBD dimer assembly complex with 2S,4R-4-methylglutamate

Experimental Data Snapshot

  • Resolution: 1.27 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Structural basis of kainate subtype glutamate receptor desensitization.

Meyerson, J.R.Chittori, S.Merk, A.Rao, P.Han, T.H.Serpe, M.Mayer, M.L.Subramaniam, S.

(2016) Nature 537: 567-571

  • DOI: https://doi.org/10.1038/nature19352
  • Primary Citation of Related Structures:  
    5CMK, 5CMM, 5KUF, 5KUH

  • PubMed Abstract: 

    Glutamate receptors are ligand-gated tetrameric ion channels that mediate synaptic transmission in the central nervous system. They are instrumental in vertebrate cognition and their dysfunction underlies diverse diseases. In both the resting and desensitized states of AMPA and kainate receptor subtypes, the ion channels are closed, whereas the ligand-binding domains, which are physically coupled to the channels, adopt markedly different conformations. Without an atomic model for the desensitized state, it is not possible to address a central problem in receptor gating: how the resting and desensitized receptor states both display closed ion channels, although they have major differences in the quaternary structure of the ligand-binding domain. Here, by determining the structure of the kainate receptor GluK2 subtype in its desensitized state by cryo-electron microscopy (cryo-EM) at 3.8 Å resolution, we show that desensitization is characterized by the establishment of a ring-like structure in the ligand-binding domain layer of the receptor. Formation of this 'desensitization ring' is mediated by staggered helix contacts between adjacent subunits, which leads to a pseudo-four-fold symmetric arrangement of the ligand-binding domains, illustrating subtle changes in symmetry that are important for the gating mechanism. Disruption of the desensitization ring is probably the key switch that enables restoration of the receptor to its resting state, thereby completing the gating cycle.

  • Organizational Affiliation

    Laboratory of Cell Biology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland 20892, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, kainate 2259Rattus norvegicusHomo sapiens
This entity is chimeric
Mutation(s): 4 
Gene Names: Grik2Glur6GRIK2GLUR6
Membrane Entity: Yes 
Find proteins for P42260 (Rattus norvegicus)
Explore P42260 
Go to UniProtKB:  P42260
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42260
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SYM

Download Ideal Coordinates CCD File 
C6 H10 N O4
Experimental Data & Validation

Experimental Data

  • Resolution: 1.27 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.308α = 90
b = 52.308β = 90
c = 170.923γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-09-07
    Changes: Database references
  • Version 1.2: 2016-09-14
    Changes: Database references
  • Version 1.3: 2016-10-05
    Changes: Database references
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description