5KC8 | pdb_00005kc8

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

• PDB DOI: https://doi.org/10.2210/pdb5KC8/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2016-06-05 Released: 2016-07-27 
• Deposition Author(s): Elegheert, J., Clay, J.E., Siebold, C., Aricescu, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.218 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

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

• PubMed: 27418511 
• 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.

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Organizational Affiliation: 
• Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232-0615, USA.
Neurobiology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan. [e-mail] [e-mail].
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.74 kDa 
• Atom Count: 3,394 
• Modeled Residue Count: 398 
• Deposited Residue Count: 429 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, delta-2	A	429	Homo sapiens	Mutation(s): 0  Gene Names: GRID2, GLURD2
UniProt & NIH Common Fund Data Resources
Find proteins for O43424 (Homo sapiens) Explore O43424  Go to UniProtKB:  O43424
PHAROS:  O43424 GTEx:  ENSG00000152208

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.218 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.1	α = 90
b = 79.16	β = 90
c = 246.69	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-27 
Deposition Author(s): Elegheert, J., Clay, J.E., Siebold, C., Aricescu, A.R.

Revision History  

• 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
• Version 1.3: 2024-10-23
  Changes: Structure summary