9C5Z | pdb_00009c5z

Structure of Ligand binding and transmembrane domains of kainate receptor Gluk2 in apo state

• PDB DOI: https://doi.org/10.2210/pdb9C5Z/pdb
• EM Map EMD-45238: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-06-07 Released: 2025-07-02 
• Deposition Author(s): Changping, Z., Nami, T.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.63 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural dynamics of GluK2 kainate receptors in apo and partial agonist bound states

Changping, Z., Guadalupe, S., Nami, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 411.66 kDa 
• Atom Count: 11,451 
• Modeled Residue Count: 1,442 
• Deposited Residue Count: 3,632 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, kainate 2	A, B, C, D	908	Rattus norvegicus	Mutation(s): 0  Gene Names: Grik2, Glur6
UniProt
Find proteins for P42260 (Rattus norvegicus) Explore P42260  Go to UniProtKB:  P42260
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P42260-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth B], H [auth C], I [auth C], J [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.63 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.5.0
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Changping, Z., Nami, T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R35GM147266-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	3R35GM147266-01S1

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release