4U4F

Structure of GluA2* in complex with partial agonist (S)-5-Nitrowillardiine

• PDB DOI: https://doi.org/10.2210/pdb4U4F/pdb

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


• Deposited: 2014-07-23 Released: 2014-08-27 
• 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: 4.79 Å
• R-Value Free: 0.262 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 

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: 371.42 kDa 
• Atom Count: 24,067 
• 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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NWD	H [auth A], I [auth B], J [auth C], L [auth D]	3-(5-nitro-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine C7 H8 N4 O6 IEBVITXSHAFLJR-VKHMYHEASA-N
NAG	K [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NWD	BindingDB:  4U4F	Ki: 115 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.79 Å
• R-Value Free: 0.262 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.374	α = 90
b = 166.575	β = 90
c = 566.604	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-08-27 
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: 2014-08-27
  Type: Initial release
  
• Version 1.1: 2014-10-01
  Changes: Database references
• Version 2.0: 2017-09-13
  Changes: Atomic model, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 2.1: 2017-11-22
  Changes: Refinement description
• Version 2.2: 2019-12-18
  Changes: Author supporting evidence
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
• Version 3.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary