4U4G

Structure of GluA2* in complex with competitive antagonist ZK 200775

• PDB DOI: https://doi.org/10.2210/pdb4U4G/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2014-07-23 Released: 2014-10-22 
• Deposition Author(s): Yelshanskaya, M.V., Li, M., 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: 4.49 Å
• R-Value Free: 0.248 
• R-Value Work: 0.217 
• R-Value Observed: 0.218 

Literature

Structure of an agonist-bound ionotropic glutamate receptor.

Yelshanskaya, M.V., Li, M., Sobolevsky, A.I.

(2014) Science 345: 1070-1074

• PubMed: 25103407 
• DOI: https://doi.org/10.1126/science.1256508
• Primary Citation of Related Structures:  
  4U4F, 4U4G


• PubMed Abstract: 
  

  Ionotropic glutamate receptors (iGluRs) mediate most excitatory neurotransmission in the central nervous system and function by opening their ion channel in response to binding of agonist glutamate. Here, we report a structure of a homotetrameric rat GluA2 receptor in complex with partial agonist (S)-5-nitrowillardiine. Comparison of this structure with the closed-state structure in complex with competitive antagonist ZK 200775 suggests conformational changes that occur during iGluR gating. Guided by the structures, we engineered disulfide cross-links to probe domain interactions that are important for iGluR gating events. The combination of structural information, kinetic modeling, and biochemical and electrophysiological experiments provides insight into the mechanism of iGluR gating.

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Organizational Affiliation: 

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

Macromolecule Content

• Total Structure Weight: 373.59 kDa 
• Atom Count: 23,812 
• Modelled Residue Count: 3,072 
• Deposited Residue Count: 3,288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor 2	A, B, C, D	822	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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G31886NL GlyCosmos:  G31886NL GlyGen:  G31886NL

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZK1	I [auth A], J [auth B], K [auth C], L [auth D]	{[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid C14 H15 F3 N3 O6 P WZMQMKNCWDCCMT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.49 Å
• R-Value Free: 0.248 
• R-Value Work: 0.217 
• R-Value Observed: 0.218 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.999	α = 90
b = 310.36	β = 94.82
c = 109.502	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-10-22 
Deposition Author(s): Yelshanskaya, M.V., Li, M., 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	NS083660

Revision History  

• Version 1.0: 2014-10-22
  Type: Initial release
  
• Version 1.1: 2015-02-11
  Changes: Advisory
• Version 1.2: 2016-12-21
  Changes: Structure summary
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence
• Version 1.4: 2017-11-22
  Changes: Refinement description
• Version 1.5: 2019-12-18
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary