6XSR

Crystal structure of GluA2 AMPA receptor in complex with trans-4-butylcyclohexane carboxylic acid (4-BCCA) inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6XSR/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2020-07-16 Released: 2020-12-30 
• Deposition Author(s): Yelshanskaya, M.V., Singh, A.K., Sobolevsky, A.I.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.25 Å
• R-Value Free: 0.296 
• R-Value Work: 0.260 
• R-Value Observed: 0.262 

Literature

Structural basis of AMPA receptor inhibition by trans-4-butylcyclohexane carboxylic acid.

Yelshanskaya, M.V., Singh, A.K., Narangoda, C., Williams, R.S.B., Kurnikova, M.G., Sobolevsky, A.I.

(2022) Br J Pharmacol 179: 3628-3644

• PubMed: 32959886 
• DOI: https://doi.org/10.1111/bph.15254
• Primary Citation of Related Structures:  
  6XSR


• PubMed Abstract: 
  

  AMPA receptors, which shape excitatory postsynaptic currents and are directly involved in overactivation of synaptic function during seizures, represent a well-accepted target for anti-epileptic drugs. Trans-4-butylcyclohexane carboxylic acid (4-BCCA) has emerged as a new promising anti-epileptic drug in several in vitro and in vivo seizure models, but the mechanism of its action remained unknown. The purpose of this study is to characterize structure and dynamics of 4-BCCA interaction with AMPA receptors.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 363.86 kDa 
• Atom Count: 23,775 
• Modelled Residue Count: 3,088 
• Deposited Residue Count: 3,232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor 2	A, B, C, D	808	Rattus norvegicus	Mutation(s): 0  Gene Names: Gria2, Glur2 Membrane Entity: Yes
UniProt
Find proteins for P19491 (Rattus norvegicus) Explore P19491  Go to UniProtKB:  P19491

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], G [auth B], H [auth C], J [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
V8G (Subject of Investigation/LOI)	F [auth A], I [auth C]	trans-4-butylcyclohexane-1-carboxylic acid C11 H20 O2 BALGERHMIXFENA-MGCOHNPYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.25 Å
• R-Value Free: 0.296 
• R-Value Work: 0.260 
• R-Value Observed: 0.262 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.79	α = 90
b = 110.4	β = 90
c = 600.14	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-30 
Deposition Author(s): Yelshanskaya, M.V., Singh, A.K., Sobolevsky, A.I.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01 NS083660

Revision History  

• Version 1.0: 2020-12-30
  Type: Initial release
  
• Version 1.1: 2022-06-29
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description