9OOO | pdb_00009ooo

Human delta 2 receptor with R710W Cerebellar Ataxia mutation in the apo closed state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.68 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


Literature

Delta-type glutamate receptors are ligand-gated ion channels.

Wang, H.Ahmed, F.Khau, J.Mondal, A.K.Twomey, E.C.

(2025) Nature 647: 1063-1071

  • DOI: https://doi.org/10.1038/s41586-025-09610-x
  • Primary Citation of Related Structures:  
    9NWO, 9NWP, 9NWQ, 9OOO, 9OOP

  • PubMed Abstract: 

    Delta-type ionotropic glutamate receptors (iGluRs), or GluDs, are members of the iGluR ligand-gated ion channel family, yet their function remains enigmatic 1 . Although GluDs are widely expressed in the brain, play key roles in synaptic organization, and harbor disease-linked mutations, whether they retain iGluR-like channel function is debated as currents have not been directly observed 2,3 . Here, we define GluDs as ligand-gated ion channels that are tightly regulated in cellular contexts by purifying human GluD2 (hGluD2) and directly characterizing its structure and function using cryo-electron microscopy (cryoEM) and bilayer recordings. We show that hGluD2 is activated by D-serine and γ-aminobutyric acid (GABA), with augmented activation at physiological temperatures. We reveal that hGluD2 contains an ion channel directly coupled to clamshell-like ligand-binding domains (LBDs), which are coordinated by the amino terminal domain (ATD) above the ion channel. Ligand binding triggers channel opening via an asymmetric mechanism, and a cerebellar ataxia point mutation in the LBD rearranges the receptor architecture and induces leak currents. Our findings demonstrate that GluDs possess the intrinsic biophysical properties of ligand-gated ion channels, reconciling prior conflicting observations to establish a framework for understanding their cellular regulation and for developing therapies targeting GluD2.


  • Organizational Affiliation
    • Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, delta-2
A, B, C, D
836Homo sapiensMutation(s): 1 
Gene Names: GRID2GLURD2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O43424 (Homo sapiens)
Explore O43424 
Go to UniProtKB:  O43424
PHAROS:  O43424
GTEx:  ENSG00000152208 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43424
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM154904

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-24
    Type: Initial release
  • Version 1.1: 2025-10-01
    Changes: Data collection, Database references
  • Version 1.2: 2025-12-10
    Changes: Data collection, Database references