5KCA | pdb_00005kca

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: 3.10 Å
  • R-Value Free: 
    0.231 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5KCA

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 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.

Macromolecule Content 

  • Total Structure Weight: 97.28 kDa 
  • Atom Count: 6,332 
  • Modeled Residue Count: 807 
  • Deposited Residue Count: 878 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cerebellin-1,Cerebellin-1,Cerebellin-1,Glutamate receptor ionotropic, delta-2878Homo sapiensMutation(s): 0 
Gene Names: CBLN1GRID2GLURD2
UniProt & NIH Common Fund Data Resources
Find proteins for O43424 (Homo sapiens)
Explore O43424 
Go to UniProtKB:  O43424
PHAROS:  O43424
GTEx:  ENSG00000152208 
Find proteins for P23435 (Homo sapiens)
Explore P23435 
Go to UniProtKB:  P23435
PHAROS:  P23435
GTEx:  ENSG00000102924 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP23435O43424
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA

Query on CA



Download:Ideal Coordinates CCD File
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.231 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.68α = 90
b = 142.68β = 90
c = 276.14γ = 120
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: 2024-01-10
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-09
    Changes: Structure summary