1.7 A resolution structure of gephyrin's E-domain

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

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This is version 1.6 of the entry. See complete history


Modulation of gephyrin-glycine receptor affinity by multivalency.

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

(2014) ACS Chem Biol 9: 2554-2562

  • DOI: https://doi.org/10.1021/cb500303a
  • Primary Citation of Related Structures:  
    4PD0, 4PD1

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gephyrin419Rattus norvegicusMutation(s): 0 
Gene Names: GphnGph
EC: (PDB Primary Data), (PDB Primary Data)
Find proteins for Q03555 (Rattus norvegicus)
Explore Q03555 
Go to UniProtKB:  Q03555
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03555
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.655α = 90
b = 100.008β = 90
c = 113.695γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySchi 425/8-1

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-27
    Type: Initial release
  • Version 1.1: 2014-09-03
    Changes: Database references
  • Version 1.2: 2014-09-17
    Changes: Database references
  • Version 1.3: 2014-12-03
    Changes: Database references
  • Version 1.4: 2017-09-27
    Changes: Advisory, Author supporting evidence, Derived calculations, Other, Source and taxonomy
  • Version 1.5: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.6: 2023-09-27
    Changes: Data collection, Database references, Refinement description