5KUF

GluK2EM with 2S,4R-4-methylglutamate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1038/nature19352
  • Primary Citation of Related Structures:  

  • 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 des ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor ionotropic, kainate 2
A, B, C, D
877Rattus norvegicusMutation(s): 4 
Gene Names: Grik2 (Glur6)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
GluK2 Glutamate receptor (Kainate-subtype) in desensitized state with bound 2S,4R-4-methylglutamate
Find proteins for P42260 (Rattus norvegicus)
Go to UniProtKB:  P42260
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SYM
Query on SYM

Download SDF File 
Download CCD File 
A, B, C, D
2S,4R-4-METHYLGLUTAMATE
C6 H10 N O4
KRKRAOXTGDJWNI-DMTCNVIQSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2016-09-14
    Type: Database references
  • Version 1.2: 2016-09-28
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence, Data collection