4PD0

1.7 A resolution structure of gephyrin's E-domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Modulation of gephyrin-glycine receptor affinity by multivalency.

Maric, H.M.Kasaragod, V.B.Schindelin, H.

(2014) Acs Chem.Biol. 9: 2554-2562

  • DOI: 10.1021/cb500303a
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Gephyrin is a major determinant for the accumulation and anchoring of glycine receptors (GlyRs) and the majority of γ-aminobutyric acid type A receptors (GABAARs) at postsynaptic sites. Here we explored the interaction of gephyrin with a dimeric form ...

    Gephyrin is a major determinant for the accumulation and anchoring of glycine receptors (GlyRs) and the majority of γ-aminobutyric acid type A receptors (GABAARs) at postsynaptic sites. Here we explored the interaction of gephyrin with a dimeric form of a GlyR β-subunit receptor-derived peptide. A 2 Å crystal structure of the C-terminal domain of gephyrin (GephE) in complex with a 15-residue peptide derived from the GlyR β-subunit defined the core binding site, which we targeted with the dimeric peptide. Biophysical analyses via differential scanning calorimetry (DSC), thermofluor, and isothermal titration calorimetry (ITC) demonstrated that this dimeric ligand is capable of binding simultaneously to two receptor binding sites and that this multivalency results in a 25-fold enhanced affinity. Our study therefore suggests that the oligomeric state of gephyrin and the number of gephyrin-binding subunits in the pentameric GABAARs and GlyRs together control postsynaptic receptor clustering.


    Organizational Affiliation

    Institute of Structural Biology, Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg , Josef-Schneider-Str. 2, 97080 Würzburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gephyrin
A
419Rattus norvegicusMutation(s): 0 
Gene Names: Gphn (Gph)
Find proteins for Q03555 (Rattus norvegicus)
Go to UniProtKB:  Q03555
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.161 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 87.655α = 90.00
b = 100.008β = 90.00
c = 113.695γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySchi 425/8-1

Revision History 

  • Version 1.0: 2014-08-27
    Type: Initial release
  • Version 1.1: 2014-09-03
    Type: Database references
  • Version 1.2: 2014-09-17
    Type: Database references
  • Version 1.3: 2014-12-03
    Type: Database references
  • Version 1.4: 2017-09-27
    Type: Advisory, Author supporting evidence, Derived calculations, Other, Source and taxonomy