1YCJ

Crystal structure of the kainate receptor GluR5 ligand-binding core in complex with (S)-glutamate

• PDB DOI: https://doi.org/10.2210/pdb1YCJ/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-12-22 Released: 2005-02-01 
• Deposition Author(s): Naur, P., Vestergaard, B., Skov, L.K., Egebjerg, J., Gajhede, M., Kastrup, J.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.269 
• R-Value Work: 0.199 
• R-Value Observed: 0.203 

Starting Model: experimental

Literature

Crystal structure of the kainate receptor GluR5 ligand-binding core in complex with (S)-glutamate

Naur, P., Vestergaard, B., Skov, L.K., Egebjerg, J., Gajhede, M., Kastrup, J.S.

(2005) FEBS Lett 579: 1154-1160

• PubMed: 15710405 
• DOI: https://doi.org/10.1016/j.febslet.2005.01.012
• Primary Citation of Related Structures:  
  1YCJ


• PubMed Abstract: 
  

  The X-ray structure of the ligand-binding core of the kainate receptor GluR5 (GluR5-S1S2) in complex with (S)-glutamate was determined to 1.95 A resolution. The overall GluR5-S1S2 structure comprises two domains and is similar to the related AMPA receptor GluR2-S1S2J. (S)-glutamate binds as in GluR2-S1S2J. Distinct features are observed for Ser741, which stabilizes a highly coordinated network of water molecules and forms an interdomain bridge. The GluR5 complex exhibits a high degree of domain closure (26 degrees) relative to apo GluR2-S1S2J. In addition, GluR5-S1S2 forms a novel dimer interface with a different arrangement of the two protomers compared to GluR2-S1S2J.

---

Organizational Affiliation: 

Biostructural Research, Department of Medicinal Chemistry, Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen, Denmark.

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: 59.18 kDa 
• Atom Count: 4,491 
• Modelled Residue Count: 507 
• Deposited Residue Count: 514 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ionotropic glutamate receptor 5	A, B	257	Rattus norvegicus	Mutation(s): 0  Gene Names: GRIK1
UniProt
Find proteins for P22756 (Rattus norvegicus) Explore P22756  Go to UniProtKB:  P22756

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLU	G [auth A], H [auth A]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.269 
• R-Value Work: 0.199 
• R-Value Observed: 0.203 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.714	α = 90
b = 57.901	β = 102.51
c = 88.75	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-01 
Deposition Author(s): Naur, P., Vestergaard, B., Skov, L.K., Egebjerg, J., Gajhede, M., Kastrup, J.S.

Revision History  

• Version 1.0: 2005-02-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-08-23
  Changes: Source and taxonomy
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-13
  Changes: Structure summary