Crystal structure of gephyrin E-domain

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.202 

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This is version 1.4 of the entry. See complete history


Deciphering the structural framework of glycine receptor anchoring by gephyrin.

Kim, E.Y.Schrader, N.Smolinsky, B.Bedet, C.Vannier, C.Schwarz, G.Schindelin, H.

(2006) EMBO J 25: 1385-1395

  • DOI: https://doi.org/10.1038/sj.emboj.7601029
  • Primary Citation of Related Structures:  
    2FTS, 2FU3

  • PubMed Abstract: 

    Glycine is the major inhibitory neurotransmitter in the spinal cord and brain stem. Gephyrin is required to achieve a high concentration of glycine receptors (GlyRs) in the postsynaptic membrane, which is crucial for efficient glycinergic signal transduction. The interaction between gephyrin and the GlyR involves the E-domain of gephyrin and a cytoplasmic loop located between transmembrane segments three and four of the GlyR beta subunit. Here, we present crystal structures of the gephyrin E-domain with and without the GlyR beta-loop at 2.4 and 2.7 A resolutions, respectively. The GlyR beta-loop is bound in a symmetric 'key and lock' fashion to each E-domain monomer in a pocket adjacent to the dimer interface. Structure-guided mutagenesis followed by in vitro binding and in vivo colocalization assays demonstrate that a hydrophobic interaction formed by Phe 330 of gephyrin and Phe 398 and Ile 400 of the GlyR beta-loop is crucial for binding.

  • Organizational Affiliation

    Department of Biochemistry, Center for Structural Biology, State University of New York, Stony Brook, NY 11794-5115, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
419Rattus norvegicusMutation(s): 0 
Gene Names: Rattus norvegicus (Norway rat)
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: 2.70 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.82α = 90
b = 156.195β = 90
c = 51.362γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references