› 5kc9

X-ray diffraction
2.3Å resolution

Crystal structure of the amino-terminal domain (ATD) of iGluR Delta-1 (GluD1)

Released:
DOI: 10.2210/pdb5kc9/pdb
Model geometry
Fit model/data
PDB entry 5kc9 coloured by chain, front view.
PDB entry 5kc9 coloured by chain, side view.
PDB entry 5kc9 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Structural basis for integration of GluD receptors within synaptic organizer complexes.
Elegheert J, Kakegawa W, Clay JE, Shanks NF, Behiels E, Matsuda K, Kohda K, Miura E, Rossmann M, Mitakidis N, Motohashi J, Chang VT, Siebold C, Greger IH, Nakagawa T, Yuzaki M, Aricescu AR
Science 353 295-9 (2016)
PMID: 27418511

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-178893 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glutamate receptor ionotropic, delta-1 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 428 amino acids
Theoretical weight: 48.4 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: Q61627 (Residues: 21-436; Coverage: 42%)
Gene name: Grid1
Sequence domains: Receptor family ligand binding region
Structure domains: Rossmann fold

Ligands and Environments

5 bound ligands:
Ligand EDO 29 x EDO
Ligand CL 14 x CL
Ligand BU1 2 x BU1
Ligand NAG 3 x NAG
Ligand PG4 1 x PG4
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P3221
Unit cell:
a: 128.42Å b: 128.42Å c: 153.23Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.201 0.199 0.227
Expression system: Homo sapiens

Quick links

Citations

29 review citations

Synaptic Neurexin Complexes: A Molecular Code for the Logic of Neural Circuits.
Südhof TC. (2017)
28 more

2 mentions without citation

Structural basis for integration of GluD receptors within synaptic organizer complexes.
Elegheert et al. (2016)
1 more