X-ray Structure of Gephyrin N-terminal Domain

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.203 

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This is version 1.3 of the entry. See complete history


X-ray crystal structure of the trimeric N-terminal domain of gephyrin.

Sola, M.Kneussel, M.Heck, I.S.Betz, H.Weissenhorn, W.

(2001) J Biol Chem 276: 25294-25301

  • DOI: https://doi.org/10.1074/jbc.M101923200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Gephyrin is a ubiquitously expressed protein that, in the central nervous system, forms a submembraneous scaffold for anchoring inhibitory neurotransmitter receptors in the postsynaptic membrane. The N- and C-terminal domains of gephyrin are homologous to the Escherichia coli enzymes MogA and MoeA, respectively, both of which are involved in molybdenum cofactor biosynthesis. This enzymatic pathway is highly conserved from bacteria to mammals, as underlined by the ability of gephyrin to rescue molybdenum cofactor deficiencies in different organisms. Here we report the x-ray crystal structure of the N-terminal domain (amino acids 2-188) of rat gephyrin at 1.9-A resolution. Gephyrin-(2-188) forms trimers in solution, and a sequence motif thought to be involved in molybdopterin binding is highly conserved between gephyrin and the E. coli protein. The atomic structure of gephyrin-(2-188) resembles MogA, albeit with two major differences. The path of the C-terminal ends of gephyrin-(2-188) indicates that the central and C-terminal domains, absent in this structure, should follow a similar 3-fold arrangement as the N-terminal region. In addition, a central beta-hairpin loop found in MogA is lacking in gephyrin-(2-188). Despite these differences, both structures show a high degree of surface charge conservation, which is consistent with their common catalytic function.

  • Organizational Affiliation

    European Molecular Biology Laboratory, 6 rue Jules Horowitz, B.P.181, 38042 Grenoble Cedex 9, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gephyrin188Rattus norvegicusMutation(s): 0 
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: 1.90 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.203 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.769α = 90
b = 65.769β = 90
c = 114.396γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-05-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references