4U5E

Crystal structure of GluA2 T625G, con-ikot-ikot snail toxin, partial agonist KA and postitive modulator (R,R)-2b complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5073 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.240 

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): 24 
Gene Names: Gria2 (Glur2)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
GluA2 Glutamate receptor (AMPA-subtype)
Find proteins for P19491 (Rattus norvegicus)
Go to UniProtKB:  P19491
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Con-ikot-ikot
E, F
90Conus striatusMutation(s): 0 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
GluA2 Glutamate receptor (AMPA-subtype)
Find proteins for P0CB20 (Conus striatus)
Go to UniProtKB:  P0CB20
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KAI
Query on KAI

Download SDF File 
Download CCD File 
A, B, C, D
3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE
KAINATE
C10 H15 N O4
VLSMHEGGTFMBBZ-OOZYFLPDSA-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 
A, B
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 %)
KAIEC50: 380000 nM (95) BINDINGDB
KAIKi: 3690 - 6300 nM (95) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5073 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.240 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 161.270α = 90.00
b = 366.690β = 90.00
c = 109.010γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
XDSdata scaling

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