5KC8

Crystal structure of the amino-terminal domain (ATD) of iGluR Delta-2 (GluD2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for integration of GluD receptors within synaptic organizer complexes.

Elegheert, J.Kakegawa, W.Clay, J.E.Shanks, N.F.Behiels, E.Matsuda, K.Kohda, K.Miura, E.Rossmann, M.Mitakidis, N.Motohashi, J.Chang, V.T.Siebold, C.Greger, I.H.Nakagawa, T.Yuzaki, M.Aricescu, A.R.

(2016) Science 353: 295-299

  • DOI: https://doi.org/10.1126/science.aae0104
  • Primary Citation of Related Structures:  
    5KC5, 5KC6, 5KC7, 5KC8, 5KC9, 5KCA

  • PubMed Abstract: 

    Ionotropic glutamate receptor (iGluR) family members are integrated into supramolecular complexes that modulate their location and function at excitatory synapses. However, a lack of structural information beyond isolated receptors or fragments thereof currently limits the mechanistic understanding of physiological iGluR signaling. Here, we report structural and functional analyses of the prototypical molecular bridge linking postsynaptic iGluR δ2 (GluD2) and presynaptic β-neurexin 1 (β-NRX1) via Cbln1, a C1q-like synaptic organizer. We show how Cbln1 hexamers "anchor" GluD2 amino-terminal domain dimers to monomeric β-NRX1. This arrangement promotes synaptogenesis and is essential for D: -serine-dependent GluD2 signaling in vivo, which underlies long-term depression of cerebellar parallel fiber-Purkinje cell (PF-PC) synapses and motor coordination in developing mice. These results lead to a model where protein and small-molecule ligands synergistically control synaptic iGluR function.


  • Organizational Affiliation

    Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, delta-2429Homo sapiensMutation(s): 0 
Gene Names: GRID2GLURD2
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: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.1α = 90
b = 79.16β = 90
c = 246.69γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-03
    Changes: Structure summary
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description