4U5D

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.58 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.258 

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Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1126/science.1258409
  • Primary Citation of Related Structures:  
    4U5B, 4U5C, 4U5D, 4U5E, 4U5F, 4U5G, 4U5H

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor 2
A, B, C, D
814Rattus norvegicusMutation(s): 23 
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
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Con-ikot-ikot
E, F
90Conus striatusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0CB20 (Conus striatus)
Explore P0CB20 
Go to UniProtKB:  P0CB20
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CB20
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 
I [auth A],
L [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 
H [auth A],
K [auth B],
N [auth C],
P [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
KAI
Query on KAI

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
O [auth D]
3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE
C10 H15 N O4
VLSMHEGGTFMBBZ-OOZYFLPDSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
KAI BindingDB:  4U5D Ki: min: 3690, max: 1.22e+4 (nM) from 4 assay(s)
EC50: min: 1.06e+4, max: 3.80e+5 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.58 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.258 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.51α = 90
b = 367.58β = 90
c = 109.38γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2014-08-27
    Changes: Database references
  • Version 1.2: 2014-10-01
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Refinement description, Structure summary
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Structure summary