6LU9 | pdb_00006lu9

Rat ionotropic Glutamate Delta-2 receptor in complex with 7-CKA and Calcium


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6LU9

This is version 1.2 of the entry. See complete history

Literature

The architecture of GluD2 ionotropic delta glutamate receptor elucidated by cryo-EM.

Burada, A.P.Vinnakota, R.Kumar, J.

(2020) J Struct Biol 211: 107546-107546

  • DOI: https://doi.org/10.1016/j.jsb.2020.107546
  • Primary Citation Related Structures: 
    6LU9

  • PubMed Abstract: 

    GluD2 receptor belongs to the orphan delta family of glutamate receptor ion channels. These receptors play key roles in synaptogenesis and synaptic plasticity and are associated with multiple neuronal disorders like schizophrenia, autism spectrum disorder, cerebellar ataxia, intellectual disability, paraplegia, retinal dystrophy, etc. Despite the importance of these receptors in CNS, insights into full-length GluD2 receptor structure is missing till-date. Here we report cryo-electron microscopy structure of the rat GluD2 receptor in the presence of calcium ions and the ligand 7-chlorokynurenic acid, elucidating its 3D architecture. The structure reveals a non-swapped architecture at the extracellular amino-terminal (ATD), and ligand-binding domain (LBD) interface similar to that observed in GluD1; however, the organization and arrangement of the ATD and LBD domains in GluD2 are unique. While our results demonstrate that non-swapped architecture is conserved in the delta receptor family, they also highlight the differences that exist between the two member receptors; GluD1 and GluD2.


  • Organizational Affiliation
    • Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University, Pune, Maharashtra 411007, India.

Macromolecule Content 

  • Total Structure Weight: 394.77 kDa 
  • Atom Count: 20,992 
  • Modeled Residue Count: 2,640 
  • Deposited Residue Count: 3,508 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, delta-2
A, B, C, D
877Rattus norvegicusMutation(s): 0 
Gene Names: Grid2
Membrane Entity: Yes 
UniProt
Find proteins for Q63226 (Rattus norvegicus)
Explore Q63226 
Go to UniProtKB:  Q63226
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63226
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.16
RECONSTRUCTIONcryoSPARCv2.13

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustIndiaIA/I/13/2/5010023

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Structure summary