5L1G

AMPA subtype ionotropic glutamate receptor GluA2 in complex with GYKI-Br


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.51 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Bases of Noncompetitive Inhibition of AMPA-Subtype Ionotropic Glutamate Receptors by Antiepileptic Drugs.

Yelshanskaya, M.V.Singh, A.K.Sampson, J.M.Narangoda, C.Kurnikova, M.Sobolevsky, A.I.

(2016) Neuron 91: 1305-1315

  • DOI: https://doi.org/10.1016/j.neuron.2016.08.012
  • Primary Citation of Related Structures:  
    5L1B, 5L1E, 5L1F, 5L1G, 5L1H

  • PubMed Abstract: 

    Excitatory neurotransmission plays a key role in epileptogenesis. Correspondingly, AMPA-subtype ionotropic glutamate receptors, which mediate the majority of excitatory neurotransmission and contribute to seizure generation and spread, have emerged as promising targets for epilepsy therapy. The most potent and well-tolerated AMPA receptor inhibitors act via a noncompetitive mechanism, but many of them produce adverse side effects. The design of better drugs is hampered by the lack of a structural understanding of noncompetitive inhibition. Here, we report crystal structures of the rat AMPA-subtype GluA2 receptor in complex with three noncompetitive inhibitors. The inhibitors bind to a novel binding site, completely conserved between rat and human, at the interface between the ion channel and linkers connecting it to the ligand-binding domains. We propose that the inhibitors stabilize the AMPA receptor closed state by acting as wedges between the transmembrane segments, thereby preventing gating rearrangements that are necessary for ion channel opening.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor 2
A, B, C, D
803Rattus norvegicusMutation(s): 4 
Gene Names: Gria2Glur2
Membrane Entity: Yes 
UniProt
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19491
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P19491-1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GYB
Query on GYB

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
I [auth B],
K [auth C],
M [auth D]
(8R)-5-(4-amino-3-bromophenyl)-N,8-dimethyl-8,9-dihydro-2H,7H-[1,3]dioxolo[4,5-h][2,3]benzodiazepine-7-carboxamide
C19 H19 Br N4 O3
OZUDBWJNUXUTGY-SNVBAGLBSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C],
L [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.51 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.79α = 90
b = 110.4β = 90
c = 600.14γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2016-11-02
    Changes: Non-polymer description
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary