Structural characterization of gephyrin by AFM and SAXS reveals a mixture of compact and extended states

Acta Crystallogr D Biol Crystallogr. 2013 Oct;69(Pt 10):2050-60. doi: 10.1107/S0907444913018714. Epub 2013 Sep 20.


Gephyrin is a trimeric protein involved in the final steps of molybdenum-cofactor (Moco) biosynthesis and in the clustering of inhibitory glycine and GABAA receptors at postsynaptic specializations. Each protomer consists of stably folded domains (referred to as the G and E domains) located at either terminus and connected by a proteolytically sensitive linker of ∼150 residues. Both terminal domains can oligomerize in their isolated forms; however, in the context of the full-length protein only the G-domain trimer is permanently present, whereas E-domain dimerization is prevented. Atomic force microscopy (AFM) and small-angle X-ray scattering (SAXS) reveal a high degree of flexibility in the structure of gephyrin. The results imply an equilibrium between compact and extended conformational states in solution, with a preference for compact states. CD spectroscopy suggests that a partial compaction is achieved by interactions of the linker with the G and E domains. Taken together, the data provide a rationale for the role of the linker in the overall structure and the conformational dynamics of gephyrin.

Keywords: GABAA receptor; Moco biosynthesis; atomic force microscopy; ensemble-optimization method; gephyrin; glycine receptor; intrinsic disorder; receptor clustering; single-molecule analysis; small-angle X-ray scattering.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Carrier Proteins / chemistry*
  • Carrier Proteins / genetics
  • Carrier Proteins / ultrastructure*
  • Circular Dichroism
  • Coenzymes / biosynthesis
  • Coenzymes / chemistry
  • Crystallography, X-Ray
  • Escherichia coli Proteins / genetics
  • Genetic Variation
  • Membrane Proteins / chemistry*
  • Membrane Proteins / genetics
  • Membrane Proteins / ultrastructure*
  • Metalloproteins / biosynthesis
  • Metalloproteins / chemistry
  • Microscopy, Atomic Force / methods
  • Molecular Dynamics Simulation
  • Molybdenum Cofactors
  • Neural Inhibition / genetics
  • Protein Conformation
  • Protein Folding
  • Protein Multimerization
  • Proteolysis
  • Pteridines / chemistry
  • Rats
  • Receptors, GABA-A / chemistry
  • Receptors, GABA-A / genetics
  • Receptors, Glycine / chemistry
  • Receptors, Glycine / genetics
  • Scattering, Small Angle*
  • X-Ray Diffraction / methods*


  • Carrier Proteins
  • Coenzymes
  • Escherichia coli Proteins
  • Membrane Proteins
  • Metalloproteins
  • Mog protein, E coli
  • Molybdenum Cofactors
  • Pteridines
  • Receptors, GABA-A
  • Receptors, Glycine
  • gephyrin
  • molybdenum cofactor

Associated data

  • PDB/1JLJ
  • PDB/2FTS