4U5C

Crystal structure of GluA2, con-ikot-ikot snail toxin, partial agonist FW and postitive modulator (R,R)-2b complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6883 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

X-ray structures of AMPA receptor-cone snail toxin complexes illuminate activation mechanism.

Chen, L.Durr, K.L.Gouaux, E.

(2014) Science 345: 1021-1026

  • DOI: 10.1126/science.1258409
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • AMPA-sensitive glutamate receptors are crucial to the structural and dynamic properties of the brain, to the development and function of the central nervous system, and to the treatment of neurological conditions from depression to cognitive impairme ...

    AMPA-sensitive glutamate receptors are crucial to the structural and dynamic properties of the brain, to the development and function of the central nervous system, and to the treatment of neurological conditions from depression to cognitive impairment. However, the molecular principles underlying AMPA receptor activation have remained elusive. We determined multiple x-ray crystal structures of the GluA2 AMPA receptor in complex with a Conus striatus cone snail toxin, a positive allosteric modulator, and orthosteric agonists, at 3.8 to 4.1 angstrom resolution. We show how the toxin acts like a straightjacket on the ligand-binding domain (LBD) "gating ring," restraining the domains via both intra- and interdimer cross-links such that agonist-induced closure of the LBD "clamshells" is transduced into an irislike expansion of the gating ring. By structural analysis of activation-enhancing mutants, we show how the expansion of the LBD gating ring results in pulling forces on the M3 helices that, in turn, are coupled to ion channel gating.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2
A, B, C, D
814Rattus norvegicusMutation(s): 23 
Gene Names: Gria2 (Glur2)
Find proteins for P19491 (Rattus norvegicus)
Go to UniProtKB:  P19491
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Con-ikot-ikot
E, F
90Conus striatusMutation(s): 0 
Find proteins for P0CB20 (Conus striatus)
Go to UniProtKB:  P0CB20
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FWD
Query on FWD

Download SDF File 
Download CCD File 
A, B, C, D
2-AMINO-3-(5-FLUORO-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-PROPIONIC ACID
FLUORO-WILLARDIINE
C7 H8 F N3 O4
DBWPFHJYSTVBCZ-BYPYZUCNSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
FWF
Query on FWF

Download SDF File 
Download CCD File 
B, D
N,N'-[biphenyl-4,4'-diyldi(2R)propane-2,1-diyl]dipropane-2-sulfonamide
C24 H36 N2 O4 S2
HGLQSTHVRKGLQP-PMACEKPBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FWDKi: 4 nM (95) BINDINGDB
FWDEC50: 460 nM (95) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6883 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 163.070α = 90.00
b = 364.780β = 90.00
c = 109.750γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-07-25 
  • Released Date: 2014-08-13 
  • Deposition Author(s): Chen, L., Gouaux, E.

Revision History 

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2014-08-27
    Type: Database references
  • Version 1.2: 2014-10-01
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary