5KCA

Crystal structure of the Cbln1 C1q domain trimer in complex with the amino-terminal domain (ATD) of iGluR Delta-2 (GluD2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1126/science.aae0104
  • Primary Citation of Related Structures:  

  • 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 there ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cerebellin-1,Cerebellin-1,Cerebellin-1,Glutamate receptor ionotropic, delta-2
A
878Homo sapiensMutation(s): 0 
Gene Names: CBLN1, GRID2 (GLURD2)
Find proteins for P23435 (Homo sapiens)
Go to Gene View: CBLN1
Go to UniProtKB:  P23435
Find proteins for O43424 (Homo sapiens)
Go to Gene View: GRID2
Go to UniProtKB:  O43424
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.204 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 142.680α = 90.00
b = 142.680β = 90.00
c = 276.140γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release