4U1Y

Full length GluA2-FW-(R,R)-2b complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.270 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Structure and Dynamics of AMPA Receptor GluA2 in Resting, Pre-Open, and Desensitized States.

Durr, K.L.Chen, L.Stein, R.A.De Zorzi, R.Folea, I.M.Walz, T.Mchaourab, H.S.Gouaux, E.

(2014) Cell 158: 778-792

  • DOI: https://doi.org/10.1016/j.cell.2014.07.023
  • Primary Citation of Related Structures:  
    4U1O, 4U1W, 4U1X, 4U1Y, 4U1Z, 4U21, 4U22, 4U23, 4U2P, 4U2Q, 4U2R

  • PubMed Abstract: 

    Ionotropic glutamate receptors (iGluRs) mediate the majority of fast excitatory signaling in the nervous system. Despite the profound importance of iGluRs to neurotransmission, little is known about the structures and dynamics of intact receptors in distinct functional states. Here, we elucidate the structures of the intact GluA2 AMPA receptor in an apo resting/closed state, in an activated/pre-open state bound with partial agonists and a positive allosteric modulator, and in a desensitized/closed state in complex with fluorowilliardiine. To probe the conformational properties of these states, we carried out double electron-electron resonance experiments on cysteine mutants and cryoelectron microscopy studies. We show how agonist binding modulates the conformation of the ligand-binding domain "layer" of the intact receptors and how, upon desensitization, the receptor undergoes large conformational rearrangements of the amino-terminal and ligand-binding domains. We define mechanistic principles by which to understand antagonism, activation, and desensitization in AMPA iGluRs.


  • Organizational Affiliation

    Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor 2
A, B, C, D
819Rattus norvegicusMutation(s): 15 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FWF
Query on FWF

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
N,N'-[biphenyl-4,4'-diyldi(2R)propane-2,1-diyl]dipropane-2-sulfonamide
C24 H36 N2 O4 S2
HGLQSTHVRKGLQP-PMACEKPBSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
L [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
FWD
Query on FWD

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
K [auth C],
M [auth D]
2-AMINO-3-(5-FLUORO-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-PROPIONIC ACID
C7 H8 F N3 O4
DBWPFHJYSTVBCZ-BYPYZUCNSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
FWD BindingDB:  4U1Y Ki: min: 4, max: 25 (nM) from 2 assay(s)
EC50: min: 460, max: 463 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.270 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.25α = 90
b = 151.44β = 90
c = 330.49γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2016-04-06
    Changes: Source and taxonomy
  • Version 1.3: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Structure summary