8GC5

Domoate-bound GluK2 kainate receptors in non-active conformation

Summary for 8GC5

• Entry DOI: 10.2210/pdb8gc5/pdb
• EMDB information: 29929
• Descriptor: Glutamate receptor ionotropic, kainate 2, alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (7 entities in total)
• Functional Keywords: ion channel, glutamate kainate receptor 2, homotetramer, membrane protein
• Biological source: Rattus norvegicus (Norway rat)
• Total number of polymer chains: 4
• Total formula weight: 404438.20

Authors

Bogdanovic, N.,Tajima, N. (deposition date: 2023-03-01, release date: 2024-03-13, Last modification date: 2025-09-24)

Primary citation

Segura-Covarrubias, G.,Zhou, C.,Bogdanovic, N.,Zhang, L.,Tajima, N.
Structural basis of GluK2 kainate receptor activation by a partial agonist.
Nat.Struct.Mol.Biol., 32:1456-1469, 2025

PubMed Abstract: Kainate receptors (KARs) belong to the family of ionotropic glutamate receptors that regulate neurotransmitter release and excitatory synaptic transmission in the central nervous system. Despite their critical roles in synaptic signaling and disease, the detailed gating mechanisms of KARs are not completely understood. Here we present cryo-electron microscopy structures of homomeric rat GluK2 KAR in an unliganded apo state and in complexes with a partial agonist, domoate. Partial agonist-bound GluK2 populates multiple conformations, including intermediate and desensitized states. Moreover, we demonstrate that the N-glycans at the amino-terminal domain-ligand binding domain (LBD) interface modulate receptor gating properties by interfering with cation binding at the LBD dimer interface. Together, these results provide insights into the unique gating mechanisms of KARs.

PubMed: 40442317
DOI: 10.1038/s41594-025-01566-w

Experimental method

ELECTRON MICROSCOPY (3.93 Å)